22-Sep-2005 Reduced warfarin requirement population 22-Sep-2005 OREGEC00000 OREGES00010 OREGET00006 smontgom 79001 VKORC1 NCBI 1 POSITIVE OUTCOME 15930419 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000002 REGULATORY HAPLOTYPE 22-Sep-2005 0 reference_sequence gcacagtggctcacgcctgtaatcccagcactttaggaagccaaggagggTggatcatgaggtcaggagtttgagaccagcctggccaatatggtgaaacc 0 false GERMLINE 0 variant_sequence gcacagtggctcacgcctgtaatcccagcactttaggaagccaaggagggCggatcatgaggtcaggagtttgagaccagcctggccaatatggtgaaacc 0 false 22-Sep-2005 0 reference_sequence atccctctgggaagtcaagcaagagaagacctgaaaaacaaccattggccGggtgcggtggctcacgcctataatcctagcattttgggaggccgaggtgg 0 false GERMLINE 0 variant_sequence atccctctgggaagtcaagcaagagaagacctgaaaaacaaccattggccAggtgcggtggctcacgcctataatcctagcattttgggaggccgaggtgg 0 false 22-Sep-2005 0 reference_sequence catggaatcctgacgtggccaaaggtgcccggtgccaggagatcatcgacCcttggactaggatgggaggtcggggaacagaggatagcccaggtggcttc 0 false GERMLINE 0 variant_sequence catggaatcctgacgtggccaaaggtgcccggtgccaggagatcatcgacTcttggactaggatgggaggtcggggaacagaggatagcccaggtggcttc 0 false 22-Sep-2005 0 reference_sequence atgcaatcttggtgatccacacagctgacagccagctagctgctcatcacGgagcgtcctgcgggtggggatgtggggaggtaactaacaggagtctttta 0 false GERMLINE 0 variant_sequence atgcaatcttggtgatccacacagctgacagccagctagctgctcatcacCgagcgtcctgcgggtggggatgtggggaggtaactaacaggagtctttta 0 false 22-Sep-2005 0 reference_sequence tcacccttcccagctccagagaaggcatcactgagggaggcccagcaccaCggtcctggctgacacatggttcagacttggccgatttatttaagaaattt 0 false GERMLINE 0 variant_sequence tcacccttcccagctccagagaaggcatcactgagggaggcccagcaccaTggtcctggctgacacatggttcagacttggccgatttatttaagaaattt 0 false 23-Sep-2005 High warfarin requirement group 23-Sep-2005 OREGEC00000 OREGES00010 OREGET00006 smontgom 79001 VKORC1 NCBI 2 POSITIVE OUTCOME 15930419 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000001 REGULATORY HAPLOTYPE 23-Sep-2005 0 reference_sequence gcacagtggctcacgcctgtaatcccagcactttaggaagccaaggagggTggatcatgaggtcaggagtttgagaccagcctggccaatatggtgaaacc 0 false GERMLINE 0 variant_sequence gcacagtggctcacgcctgtaatcccagcactttaggaagccaaggagggTggatcatgaggtcaggagtttgagaccagcctggccaatatggtgaaacc 0 false 23-Sep-2005 0 reference_sequence atccctctgggaagtcaagcaagagaagacctgaaaaacaaccattggccGggtgcggtggctcacgcctataatcctagcattttgggaggccgaggtgg 0 false GERMLINE 0 variant_sequence atccctctgggaagtcaagcaagagaagacctgaaaaacaaccattggccGggtgcggtggctcacgcctataatcctagcattttgggaggccgaggtgg 0 false 23-Sep-2005 0 reference_sequence catggaatcctgacgtggccaaaggtgcccggtgccaggagatcatcgacCcttggactaggatgggaggtcggggaacagaggatagcccaggtggcttc 0 false GERMLINE 0 variant_sequence catggaatcctgacgtggccaaaggtgcccggtgccaggagatcatcgacCcttggactaggatgggaggtcggggaacagaggatagcccaggtggcttc 0 false 23-Sep-2005 0 reference_sequence atgcaatcttggtgatccacacagctgacagccagctagctgctcatcacGgagcgtcctgcgggtggggatgtggggaggtaactaacaggagtctttta 0 false GERMLINE 0 variant_sequence atgcaatcttggtgatccacacagctgacagccagctagctgctcatcacGgagcgtcctgcgggtggggatgtggggaggtaactaacaggagtctttta 0 false 23-Sep-2005 0 reference_sequence tcacccttcccagctccagagaaggcatcactgagggaggcccagcaccaCggtcctggctgacacatggttcagacttggccgatttatttaagaaattt 0 false GERMLINE 0 variant_sequence tcacccttcccagctccagagaaggcatcactgagggaggcccagcaccaCggtcctggctgacacatggttcagacttggccgatttatttaagaaattt 0 false The CT60 polymorphism is 3' of the CTLA4 gene and is associated to Grave's Disease. The allele was confirmed using ASTQ (allele-specific transcript quantification) to reduce expression. 19-Sep-2005 smontgom 19-Sep-2005 19-Sep-2005 OREGEC00001 OREGES00009 OREGET00004 smontgom 1493 CTLA4 NCBI 3 POSITIVE OUTCOME 12724780 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000000 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 19-Sep-2005 0 reference_sequence ttttgatttcttcaccactatttgggatataacAtgggttaacacagacata 0 false rs3087243 dbSNP GERMLINE 0 variant_sequence ttttgatttcttcaccactatttgggatataacGtgggttaacacagacata 0 false 23-Sep-2005 Upregulated 2.9 fold (No change to steady-state expression using RT-PCR) 23-Sep-2005 OREGEC00003 OREGES00012 OREGET00005 smontgom 9628 RGS6 NCBI 4 POSITIVE OUTCOME 15375002 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000003 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 23-Sep-2005 0 reference_sequence ccaggccctggacctgcggtaggaaCggtcaggaggactgcatcaggcccg 0 false rs2074647 dbSNP GERMLINE 0 variant_sequence ccaggccctggacctgcggtaggaaTggtcaggaggactgcatcaggcccg 0 false 23-Sep-2005 Unknown factor bound; Likely not AP2; Expression; T allele drives expression 2.8-fold; C allele drives expression 2.2-fold. 23-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom 3938 LCT NCBI 5 POSITIVE OUTCOME 12915462 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000004 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 23-Sep-2005 0 reference_sequence gataagataatgtagCccctggcctcaaag 0 false rs4988235 dbSNP GERMLINE 0 variant_sequence gataagataatgtagTccctggcctcaaag 0 false 23-Sep-2005 Confirmed that differential binding occured for this polymorphism. Binding occured for T allele. 23-Sep-2005 OREGEC00001 OREGES00001 OREGET00001 smontgom Confirmed binding of C/EBP Beta to binding site. 23-Sep-2005 OREGEC00002 OREGES00002 OREGET00001 smontgom 3576 IL8 NCBI 6 POSITIVE OUTCOME 15085176 0 sequence_with_flank EMPTY 0 false 0 sequence GTTGTTCAAT 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000005 1051 CEBPB NCBI REGULATORY POLYMORPHISM 23-Sep-2005 0 reference_sequence aaagaactctaactctttatataggaagtTgttcaatgttgtcagtt 0 false rs2227306 dbSNP GERMLINE 0 variant_sequence aaagaactctaactctttatataggaagtCgttcaatgttgtcagtt 0 false Test population Ethiopian 27-Sep-2005 smontgom 27-Sep-2005 Likely ETS-family binding site 27-Sep-2005 OREGEC00001 OREGES00003 OREGET00001 smontgom In the presence of TCDD enzyme this allele had altered expression activity. However, without the TCDD, the results were inconclusive (for altered expression). 27-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom 1544 CYP1A2 NCBI 11 POSITIVE OUTCOME 12920202 0 search_space ACCCTGAACCCTAAAGACAGCTGTACCTTCATCCCCAGGGACCCAGCACCCCTTCTGGCCTATCCCCAAAGAGTCACCCTGGGTCTTAGGTAGTAGGTGGAGCTGAGGGATAATGGCCCAAGGCCAAGAGTTGATCCTTCCAACTTTGTTCAGTGATCCAGCTTTCATATCAGGTGATCAGGACAACCAGGCCAATCTGATAGGGGGCGGTGTTTATAAAAAGGCCACTCACCTAGAGCCAGAAGCTCCACACCAGCCATTACAACCCTGCCAATCTCAAGCACCTGCCTCTACAGGTACCTTTCTTGGGACCAATTTACAATCTCTGGGATCCCCAACTATAGAACCTGGAAGCTAGTGGGGACAGAAAGACGGGGAGCCTGGGCTAGGTGTAGGGGTCCTGAGTTCCGGGCTTTGCTACCCAGCTCTTGACTTCTGTTTCCCGATTTTAAATGAGCAGTTTGGACTAAGCCATTTTTAAGGAGAGCGATGGGGAGGGCTTCCCCCTTAGCACAAGGGCAGCCCTGGCCCTGGCTGAAGCCCAACCCCAACCTCCAAGACTGTGAGAGGATGGGGACTCATCCCTGGAGGAGGTGCCCCTCCTGGTATTGATAAAGAATGCCCTGGGGAGGGGGCATCACAGGCTATTTGAACCAGCCCTGGGACCTTGGCCACCTCAGTGTCACTGGGTAGGGGGAACTCCTGGTCCCTTGGGTATATGGAAGGTATCAGCAGAAAGCCAGCACTGGCAGGGACTCTTTGGTACAATACCCAGCATGCATGCTGTGCCAGGGGCTGACAAGGGTGCTGTCCTTGGCTTCCCCATTTTGGAGTGGTCACTTGCCTCTACTCCAGCCCCAGAAGTGGAAACTGAGATGATGTGTGGAGGAGAGAGCCAGCGTTCATGTTGGGAATCTTGAGGCTCCTTTCCAGCTCTCAGATTCTGTGATGCTCAAAGGGTGAGCTCTGTGGGCCCAGGACGCATGGTAGATGGAGCTTAGTCTTTCTGGTATCCAGCTGGGAGCCAAGCACAGAACACGCATCAGTGTTTATCAAATGACTGAGGAAATGAATGAATGAATGTCTCCATCTCAACCCTCAGCCTGGTCCCTCCTTTTTTCCCTGCAGTTGGTACAG 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000008 UNKNOWN-ETS UNKNOWN-ETS USER DEFINED REGULATORY POLYMORPHISM 27-Sep-2005 0 reference_sequence tgagttcCgggctttgctacccag 0 false rs12720461 dbSNP GERMLINE 0 variant_sequence tgagttcTgggctttgctacccag 0 false The TATA binding protein (TBP) was demonstrated to be disrupted in the presence of the G allele resulting in 50% decreased expression from wild-type. 28-Sep-2005 smontgom 28-Sep-2005 Cell type: human hepatoma cell line, B16A2 28-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom 1548 CYP2A6 NCBI 12 POSITIVE OUTCOME 11394901 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000009 TBP TBP USER DEFINED REGULATORY POLYMORPHISM 28-Sep-2005 0 reference_sequence catccctctttttcaggcagtaTaaaggcaaaggagggg 0 false GERMLINE 0 variant_sequence catccctctttttcaggcagtaGaaaggcaaaggagggg 0 false 28-Sep-2005 When allele (G) present, CYP2A6 is expressed at 48% of wild-type activity. 28-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom ROughly two to four-fold lower affinity for nuclear extracts in the presence of the variant (G) allele. 28-Sep-2005 OREGEC00001 OREGES00001 OREGET00001 smontgom 1548 CYP2A6 NCBI 14 POSITIVE OUTCOME 14974084 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000012 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 28-Sep-2005 0 reference_sequence tgcccactgtctgttttctgtcctctgtAgatctttatataaaatgag 0 false rs4803381 dbSNP GERMLINE 0 variant_sequence tgcccactgtctgttttctgtcctctgtGgatctttatataaaatgag 0 false 28-Sep-2005 The TATATAA sequence is important for the binding of a larger DNA-complex, but a smaller complex is able to bind the upstream part of this region (TTCTGTCCTCTGTAGATCTT) 28-Sep-2005 OREGEC00001 OREGES00001 OREGET00001 smontgom 1548 CYP2A6 NCBI 15 POSITIVE OUTCOME 14974084 0 search_space TTCTGTCCTCTGTAGATCTTTATATAA 0 false 0 sequence TTCTGTCCTCTGTAGATCTTTATATAA 0 false 0 sequence_with_flank CTCACACATGTCCCCTGCCCACTGTCTGTTTTCTGTCCTCTGTAGATCTTTATATAAAATGAGAAACATAAACAACAATCATAATATTA 0 false Homo sapiens OREG0000013 REGULATORY REGION 28-Sep-2005 NF-Y pulled down search sequence. 28-Sep-2005 OREGEC00002 OREGES00005 OREGET00003 smontgom Competition eliminated with variant allele (G). 28-Sep-2005 OREGEC00001 OREGES00001 OREGET00001 smontgom Cell line: Human hepatoma HepG2. 22% reduction in activity with variant (G) allele. 28-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom 1548 CYP2A6 NCBI 19 POSITIVE OUTCOME 15247629 0 search_space GAGGATCTGGGTTGGAAACCAGCGGACAACCCTTGGGACACTTGAGATTTTTCCACCATTTGGGGGTTGTTATTACTATTTCTCCAGACCTAGCCAATCCCTCTGCCAACCGCTAACTCCAGGTACTCTTCTCCAGGTGTGGGGAAAGTTCCCCTGAAATATGGCTCTGGTCTTCCTCCCCTTCCCAATCAGAGATGGGCAGTGGAGGTTCTATGGCACCCATCCTGGCCTCACTCTGAGGTTCCAATGAGGATTCTGGGCATCAAGAGACAGCTCTGGGCAAAAGCAAAATCAAGTCAGCCCCTGGACCCAGTGCTGGGCTGCTGG 0 false 0 sequence CCAAT 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000019 4800 NFYA NCBI REGULATORY POLYMORPHISM 28-Sep-2005 0 reference_sequence ctccccttcccaAtcagagatggg 0 false GERMLINE 0 variant_sequence ctccccttcccaGtcagagatggg 0 false Neutral outcome entered. Primary authors indicate that depth of population sampling cannot only supports a minor role of this haplotype in determing the ultrarapid metabolizer group. 28-Sep-2005 smontgom 28-Sep-2005 Variant associated to ultrarapid metabolizer group. 28-Sep-2005 OREGEC00000 OREGES00010 OREGET00006 smontgom 1565 CYP2D6 NCBI 20 NEUTRAL OUTCOME 11207030 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000020 REGULATORY HAPLOTYPE 28-Sep-2005 0 reference_sequence caacttggaagaaccCggtctctacaaaaa 0 false GERMLINE 0 variant_sequence caacttggaagaaccGggtctctacaaaaa 0 false 29-Sep-2005 Cell line: HepG2 Human hepatocarcinoma 29-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom 1576 CYP3A4 NCBI 22 POSITIVE OUTCOME 14742674 0 search_space GGTACCTGGTTCATCTCATTGGGACTGGTTGGACAAGAGGGTGCAGCCCACGGAGGGTGAGCCAAAGCAGGGTGGGGCGTCGCCTCACCTGGGAAGCACAAGGGGTCGTGGAATTTTCTCCCCTACCCAAGGAAAGCCATAAGGGACTGAGCCTGAGGAACTGTGCACTCTGGCCCAGATACTGCACTTTTCCCATGGTCTTTGCAACCCGCAGACCAGGAGATTCCCTCCGGTGCCTATGCCACCAGGGCCCTGGGTTTCAAGCACAAAACTGGGCAGCCATTTGGGCAGACACCGAACTAGCTGCAGGAGTTTTTTTTTTTTTTTTTCCATACCCCATTGGCACCTGGAACGCCAGTGAGACAGAACCGTTCACTCCCCTGGAAAGGGGGCTGAAACCAGGGATCCAAGTGGTCTGGCTCGGTGGGCCCCACCCCCATGGAGCCCAGCAAACAAAGATTCACTTGGCTTGAAATTCTTGCTGCCAGCACAGCAGCAGTCTGAGATTGACCTGGGACCCTCGAACTTGGTTGGGTGCTGTGGGGGGGCATCTTCCATTGCTGAGGCTTGAGTAGGTGGTTTTACCTTCGCGGTGTAAACAAAGCTGCTGGGAAGTTTGAACTGGGTGGAGCTCACCACAGCTCAGTAAGGCCACTGTGGCCAGACTGCCTCTCTGGATTTCTCCTCTCTGGGAAGGATATCTCTGAAAAAAAGGCAGCAGCCCCAGTCAGGGACTTATAGATGAAACCCCCATCTCCCTGGGACAGAGCCCCTCGGGGAAGAGGTGGCTTCCACCATTGTGGAAGACTGTGTGGCAATTCCTCACGGATTTAGAACTAGAGATACCATTTGACCCAGCAATCCCATTACTGGGTGTATACCCATAGGATTATAAATCATTCTACTATAAAGACACATGCACACTTATGTTTATTGTAACACTATTTACAATAGCAATGACCTGGAACCAATCCAAAAGCCCATCAATGATAGACTGAATAAAGAAAATGTGGCACATATACACTGTGGAATACTATGCAGCCATAAAAAAGGATGAGTTCATGTCCTTTGCAGAGACATGGATGAAGCTGGAAACCATCATTCTCAGCAAACTAGCACAATAACAGAAAACCAAACACTGCATGTTGTCACTCATAAGTGGGAGTTAAACAATGAGAACACATGGACACAGGGAGGGGAACGTCACACACTGGGGCATGTCGGGGAGTGGGGGCCTACGGGAGGGATAGCATTAGCAGAAATACCTAATGTAGGTGACGGGTTGATGGGTGCAGCAAACCACCATGGCACATATACACCTATGTAATAAAACTGCACGTTCTGCACATGTACCCCAGAACTTAAAGTATAATTAATAATAATAATAATTTCTGGGCATGTAAGTAGCTGTCTTTCAGGTTCTACTTTGATACATATTCTGAGAGAATTAAACCTGTCAAAGAAACCTTGACTTTCAATGGCAGGCACTGGAATTGACCCTAATAATGTGTTTTGGGGTAAGCCTACTCATATTCTCAACCTGTCTGCAGTAGTCGTTAGAATCTGAACTTCCTGAAGTTCATGTGCAAAGTTGAGTTAATTGTTTAATATTCAACAAGGATTATGCCAGTAAGATGGTAGGAAAATATTAGATATGTGTCATCACTGCTGGTATTATTTAAACTGCAACATATTTTAGCTGGCTGCTGATCTCAGCCACCATGCCTGCATTTTATCTCTGTCTCGTGGTCTGCAACCTTGGAAGCTTTGAACTTAGCTCATAGAATCCTGGGCATCAAGAACATGTGGTTCTAATGGCTAGATAGGGAATGAGAGTAAAAGGATTTTGCCCACGGTCACGTGAGTAAACAACAGATTTGGAGGGGTCTGGACTACTGTGATGACTTCATTCTGACAATATGTTCCAGTTGTCCTTTCATTTCCTCCTAATCACATGTCTGGTCTGATCTGGCTGTTTCCCACCTTCCAATTCCTGCCTTCTCCAATGCTCCCTTCCGTAGGTCACTCTGTGGCTCAGAGACCCTGCTTAGCAAGCGCCCAACCTTTCAATTATTTGTTCAGTAAAACTTGAACTCATGTCTCCCCTTCTTGATAAAAAGAAAATACGTTATGTAATGTCGGGTTACTCTATAACTCTTGTCCTGTCTCTCGGCAACTACTGAACTAACTGTTTTCATATTGAGCAAACGTTTATGGAAGGACTGCCAAGAGTCAGGTACTAGGCTTGGTAATATTCCCCGTTCTCTCTAGTCAAAGCCAACACCAGCCAGACTTGCAGATCTAGGTCCCAAGCCCACTGCAGATCACAGGCCAGGGTCTGGTCTCCTCTGAGCTCCTTTGGGAGGGAAAGACAGAATTATTAACACCCATTTTGTAGATTAGGCAACTGAGGCTGAGGAAGTTTAAATAACTCAGACAGGGCCTGCACGTCAGTCATATTCCAA 0 false 0 sequence CCTGTCTGCAGTAGTCGTTAGAATCTGAACTTCCTGAAGTTCATGTGCAAAGTTGAGTTAATTGTTTAATATTCAACAAGGATTATGCCAGTAAGATGGTAGGAAAATATTAGATATGTGTCATCACTGCTGGTATTATTTAAACTGCAACATATTTTAGCTGGCTGCTGATCTCAGCCACCATGCCTGCATTTTATCTCTGTCTCGTGGTCTGCAACCTTGGAAGCTTTGAACTTAGCTCATAGAATCCTGGGCATCAAGAACATGTGGTTCTAATGGCTAGATAGGGAATGAGAGTAAAAGGATTTTGCCCACGGTCACGTGAGTAAACAACAGATTTGGAGGGGTCTGGACTACTGTGATGACTTCATTCTGACAATATGTTCCAGTTGTCCTTTCATTTCCTCCTAATCACATGTCTGGTCTGATCTGGCTGTTTCCCACCTTCCAATTCCTGCCTTCTCCAATGCTCCCTTCCGTAGGTCACTCTGTGGCTCAGAGACCCTGCTTAGCAAGCGCCCAACCTTTCAATTATTTGTTCAGTAAAACTTGAACTCATGTCTCCCCTTCTTGATAAAAAGAAAATACGTTATGTAATGTCGGGTTACTCTATAACTCTTGTCCTGTCTCTCGGCAACTACTGAACTAACTGTTTTCATATTGAGCAAACGTTTATGGAAGGACTGCCAAGAGTCAGGTACTAGGCTTGGTAATATTCCCCGTTCTCTCTAGTCAAAGCCAACACCAGCCAGACTTGCAGATCTAGGTCCCAAGCCCACTGCAGATCACAGGCCAGGGTCTGGTCTCCTCTGAGCTCCTTTGGGAGGGAAAGACAGAATTATTAACACCCATTTTGTAGATTAGGCAACTGAGGCTGAGGAAGTTTAAATAACTCAGACAGGGCCTGCACGTCAGTCATATTCCAA 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000022 REGULATORY REGION Enhancer activity reduced by 64% in presence of allele (TGT). Allele is rare in French population. Cell line is human liver. 29-Sep-2005 smontgom 29-Sep-2005 Cell line: Human liver HepG2 29-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom 29-Sep-2005 OREGEC00002 OREGES00003 OREGET00001 smontgom 1576 CYP3A4 NCBI 23 POSITIVE OUTCOME 14742674 0 search_space GTCGTTAGAATCTGAACTTCCTGAAGTTCATGTGCAAAGTTGAGTTAATTGTTTAATATTCAACAAGGATTATGCCAGTAAGATGGTAGGAAAATATTAGATATGTGTCATCACTGCTGGTATTATTTAAACTGCAACATATTTTAGCTGGCTGCTGATCTCAGCCACCATGCCTGCATTTTATCTCTGTCTCGTGGTCTGCAACCTTGGAAGCTTTGAACTTAGCTCATAGAATCCTGGGCATCAAGAACATGTGGTTCTAATGGCTAGATAGGGAATGAGAGTAAAAGGATTTTGCCCACGGTCACGTGAGTAAACAACAGATTTGGAGGGGTCTGGACTACTGTGATGACTTCATTCTGACAATATGTTCCAGTTGTCCTTTCATTTCCTCCTAATCACATGTCTGGTCTGATCTGGCTGTTTCCCACCTTCCAATTCCTGCCTTCTCCAATGCTCCCT 0 false 0 sequence CATGTG 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000023 7391 USF1 NCBI REGULATORY POLYMORPHISM 29-Sep-2005 0 reference_sequence gcatcaagaacatgtggttctaatgg 0 false GERMLINE 0 variant_sequence gcatcaagaacatgtTGTggttctaatgg 0 false Binding sequence was determined computationally as the canonical binding sequence. Only the 3' most AA sequence of the binding site was biologically tested. 30-Sep-2005 smontgom 30-Sep-2005 Antibodies to HNF-4alpha not HNF-4gamma supershifted bound complex. 30-Sep-2005 OREGEC00002 OREGES00002 OREGET00001 smontgom aagttcatgtgcaCCgttgagttaatt (AA to CC mutation in HNF-4 binding site as competitor) does not compete for binding with HNF-4 sequence. HNF-4 sequence in excess competes out complex formation. 30-Sep-2005 OREGEC00001 OREGES00003 OREGET00001 smontgom aagttcatgtgcaCCgttgagttaatt (AA to CC mutation in HNF-4 binding site) reduces enhancer activity by 19% 30-Sep-2005 OREGEC00002 OREGES00004 OREGET00002 smontgom 1576 CYP3A4 NCBI 54 POSITIVE OUTCOME 14742674 0 search_space GTCGTTAGAATCTGAACTTCCTGAAGTTCATGTGCAAAGTTGAGTTAATTGTTTAATATTCAACAAGGATTATGCCAGTAAGATGGTAGGAAAATATTAGATATGTGTCATCACTGCTGGTATTATTTAAACTGCAACATATTTTAGCTGGCTGCTGATCTCAGCCACCATGCCTGCATTTTATCTCTGTCTCGTGGTCTGCAACCTTGGAAGCTTTGAACTTAGCTCATAGAATCCTGGGCATCAAGAACATGTGGTTCTAATGGCTAGATAGGGAATGAGAGTAAAAGGATTTTGCCCACGGTCACGTGAGTAAACAACAGATTTGGAGGGGTCTGGACTACTGTGATGACTTCATTCTGACAATATGTTCCAGTTGTCCTTTCATTTCCTCCTAATCACATGTCTGGTCTGATCTGGCTGTTTCCCACCTTCCAATTCCTGCCTTCTCCAATGCTCCCT 0 false 0 sequence TCATGTGCAAAGTTGAGTT 0 false 0 sequence_with_flank GTAGTCGTTAGAATCTGAACTTCCTGAAGTTCATGTGCAAAGTTGAGTTAATTGTTTAATATTCAACA 0 false Homo sapiens OREG0000053 3172 HNF4A NCBI TRANSCRIPTION FACTOR BINDING SITE Binding sequence was determined computationally as the canonical binding sequence. Only the CTT sequence of the binding site was biologically tested. 30-Sep-2005 smontgom 30-Sep-2005 Antibodies to HNF-4alpha supershifted bound complex. 30-Sep-2005 OREGEC00002 OREGES00002 OREGET00001 smontgom ggaagctttgaaAGCagctcatagaa (CTT to AGC mutation in HNF-4 binding site as competitor) does not compete for binding with HNF-4 sequence. HNF-4 sequence in excess competes out complex formation. 30-Sep-2005 OREGEC00001 OREGES00003 OREGET00001 smontgom ggaagctttgaaAGCagctcatagaa (CTT to AGC mutation in HNF-4 binding site) reduces enhancer activity by 44% 30-Sep-2005 OREGEC00002 OREGES00004 OREGET00002 smontgom 1576 CYP3A4 NCBI 55 POSITIVE OUTCOME 14742674 0 search_space GTCGTTAGAATCTGAACTTCCTGAAGTTCATGTGCAAAGTTGAGTTAATTGTTTAATATTCAACAAGGATTATGCCAGTAAGATGGTAGGAAAATATTAGATATGTGTCATCACTGCTGGTATTATTTAAACTGCAACATATTTTAGCTGGCTGCTGATCTCAGCCACCATGCCTGCATTTTATCTCTGTCTCGTGGTCTGCAACCTTGGAAGCTTTGAACTTAGCTCATAGAATCCTGGGCATCAAGAACATGTGGTTCTAATGGCTAGATAGGGAATGAGAGTAAAAGGATTTTGCCCACGGTCACGTGAGTAAACAACAGATTTGGAGGGGTCTGGACTACTGTGATGACTTCATTCTGACAATATGTTCCAGTTGTCCTTTCATTTCCTCCTAATCACATGTCTGGTCTGATCTGGCTGTTTCCCACCTTCCAATTCCTGCCTTCTCCAATGCTCCCT 0 false 0 sequence CTTTGAACTTAGCTCATAG 0 false 0 sequence_with_flank GTCTCGTGGTCTGCAACCTTGGAAGCTTTGAACTTAGCTCATAGAATCCTGGGCATCAAG 0 false Homo sapiens OREG0000054 3172 HNF4A NCBI TRANSCRIPTION FACTOR BINDING SITE Binding sequence was determined computationally as the canonical binding sequence. Only the AAC sequence of the binding site was biologically tested. 30-Sep-2005 smontgom 30-Sep-2005 Antibodies to HNF-1 supershifted bound complex. 30-Sep-2005 OREGEC00002 OREGES00002 OREGET00001 smontgom ttaattgtttaatattcCTGaagga (AAC to CTG mutation in HNF-1 binding site as competitor) does not compete for binding with HNF-1 sequence. HNF-1 sequence in excess competes out complex formation. 30-Sep-2005 OREGEC00001 OREGES00003 OREGET00001 smontgom ttaattgtttaatattcCTGaagga (AAC to CTG mutation in HNF-1 binding site) reduces enhancer activity by 30% 30-Sep-2005 OREGEC00002 OREGES00004 OREGET00002 smontgom 1576 CYP3A4 NCBI 56 POSITIVE OUTCOME 14742674 0 search_space GTCGTTAGAATCTGAACTTCCTGAAGTTCATGTGCAAAGTTGAGTTAATTGTTTAATATTCAACAAGGATTATGCCAGTAAGATGGTAGGAAAATATTAGATATGTGTCATCACTGCTGGTATTATTTAAACTGCAACATATTTTAGCTGGCTGCTGATCTCAGCCACCATGCCTGCATTTTATCTCTGTCTCGTGGTCTGCAACCTTGGAAGCTTTGAACTTAGCTCATAGAATCCTGGGCATCAAGAACATGTGGTTCTAATGGCTAGATAGGGAATGAGAGTAAAAGGATTTTGCCCACGGTCACGTGAGTAAACAACAGATTTGGAGGGGTCTGGACTACTGTGATGACTTCATTCTGACAATATGTTCCAGTTGTCCTTTCATTTCCTCCTAATCACATGTCTGGTCTGATCTGGCTGTTTCCCACCTTCCAATTCCTGCCTTCTCCAATGCTCCCT 0 false 0 sequence TTGTTTAATATTCAACA 0 false 0 sequence_with_flank ATGTGCAAAGTTGAGTTAATTGTTTAATATTCAACAAGGATTATGCCAGTAAGA 0 false Homo sapiens OREG0000055 6927 TCF1 NCBI TRANSCRIPTION FACTOR BINDING SITE Binding sequence was determined computationally as the canonical binding sequence. Only the GTG sequence of the binding site was biologically tested. 30-Sep-2005 smontgom 30-Sep-2005 Antibodies to USF1 supershifted bound complex. 30-Sep-2005 OREGEC00002 OREGES00002 OREGET00001 smontgom gcatcaagaacatTAGgttctaatgg (GTG to TAG mutation in E-box binding site as competitor) does not compete for binding with E-box sequence. E-box sequence in excess competes out complex formation. 30-Sep-2005 OREGEC00001 OREGES00003 OREGET00001 smontgom gcatcaagaacatTAGgttctaatgg (GTG to TAG mutation in E-box binding site) reduces enhancer activity 33% 30-Sep-2005 OREGEC00002 OREGES00004 OREGET00002 smontgom 1576 CYP3A4 NCBI 57 POSITIVE OUTCOME 14742674 0 search_space GTCGTTAGAATCTGAACTTCCTGAAGTTCATGTGCAAAGTTGAGTTAATTGTTTAATATTCAACAAGGATTATGCCAGTAAGATGGTAGGAAAATATTAGATATGTGTCATCACTGCTGGTATTATTTAAACTGCAACATATTTTAGCTGGCTGCTGATCTCAGCCACCATGCCTGCATTTTATCTCTGTCTCGTGGTCTGCAACCTTGGAAGCTTTGAACTTAGCTCATAGAATCCTGGGCATCAAGAACATGTGGTTCTAATGGCTAGATAGGGAATGAGAGTAAAAGGATTTTGCCCACGGTCACGTGAGTAAACAACAGATTTGGAGGGGTCTGGACTACTGTGATGACTTCATTCTGACAATATGTTCCAGTTGTCCTTTCATTTCCTCCTAATCACATGTCTGGTCTGATCTGGCTGTTTCCCACCTTCCAATTCCTGCCTTCTCCAATGCTCCCT 0 false 0 sequence CATGTG 0 false 0 sequence_with_flank GCTCATAGAATCCTGGGCATCAAGAACATGTGGTTCTAATGGCTAGATAGGGAATGAGA 0 false Homo sapiens OREG0000056 7391 USF1 NCBI TRANSCRIPTION FACTOR BINDING SITE Binding sequence was determined computationally as the canonical binding sequence. Only the CGT sequence of the binding site was biologically tested. 30-Sep-2005 smontgom 30-Sep-2005 Antibodies to USF1 supershifted bound complex. 30-Sep-2005 OREGEC00002 OREGES00001 OREGET00001 smontgom tgcccacggtcaTAAgagtaaacaac (CGT to TAA mutation in E-box binding site as competitor) does not compete for binding with E-box sequence. E-box sequence in excess competes out complex formation. 30-Sep-2005 OREGEC00001 OREGES00001 OREGET00001 smontgom tgcccacggtcaTAAgagtaaacaac (CGT to TAA mutation in E-box binding site) reduces enhancer activity by 43% 30-Sep-2005 OREGEC00002 OREGES00004 OREGET00002 smontgom 1576 CYP3A4 NCBI 58 POSITIVE OUTCOME 14742674 0 search_space GTCGTTAGAATCTGAACTTCCTGAAGTTCATGTGCAAAGTTGAGTTAATTGTTTAATATTCAACAAGGATTATGCCAGTAAGATGGTAGGAAAATATTAGATATGTGTCATCACTGCTGGTATTATTTAAACTGCAACATATTTTAGCTGGCTGCTGATCTCAGCCACCATGCCTGCATTTTATCTCTGTCTCGTGGTCTGCAACCTTGGAAGCTTTGAACTTAGCTCATAGAATCCTGGGCATCAAGAACATGTGGTTCTAATGGCTAGATAGGGAATGAGAGTAAAAGGATTTTGCCCACGGTCACGTGAGTAAACAACAGATTTGGAGGGGTCTGGACTACTGTGATGACTTCATTCTGACAATATGTTCCAGTTGTCCTTTCATTTCCTCCTAATCACATGTCTGGTCTGATCTGGCTGTTTCCCACCTTCCAATTCCTGCCTTCTCCAATGCTCCCT 0 false 0 sequence CACGTG 0 false 0 sequence_with_flank GAGAGTAAAAGGATTTTGCCCACGGTCACGTGAGTAAACAACAGATTTGGAGGGGT 0 false Homo sapiens OREG0000057 7391 USF1 NCBI TRANSCRIPTION FACTOR BINDING SITE Binding sequence was determined computationally as the canonical binding sequence. Mutation analysis of GT in binding site did not compete out binding in gel shift competition. This is likely because the change from the canonical TG sequence wasn't significant enough (when compared to other binding sites from this reference). However, this conclusion, is in disagreement with the effect observed in the reported gene assay in vitro (where the mutation caused a reduction in activity of 47%) 30-Sep-2005 smontgom 30-Sep-2005 Antibodies to USF1 supershifted bound complex. 30-Sep-2005 OREGEC00002 OREGES00002 OREGET00001 smontgom tcctcctaatcacaGTtctggtctga (mutation in E-box binding site of TG to GT) did not compete out binding. However, binding was compete out in the presence of excess unlabelled E-box sequence. 30-Sep-2005 OREGEC00001 OREGES00003 OREGET00001 smontgom tcctcctaatcacaGTtctggtctga (mutation in E-box binding site of TG to GT) reduces enhancer activity by 47% 30-Sep-2005 OREGEC00002 OREGES00004 OREGET00002 smontgom 1576 CYP3A4 NCBI 59 POSITIVE OUTCOME 14742674 0 search_space GTCGTTAGAATCTGAACTTCCTGAAGTTCATGTGCAAAGTTGAGTTAATTGTTTAATATTCAACAAGGATTATGCCAGTAAGATGGTAGGAAAATATTAGATATGTGTCATCACTGCTGGTATTATTTAAACTGCAACATATTTTAGCTGGCTGCTGATCTCAGCCACCATGCCTGCATTTTATCTCTGTCTCGTGGTCTGCAACCTTGGAAGCTTTGAACTTAGCTCATAGAATCCTGGGCATCAAGAACATGTGGTTCTAATGGCTAGATAGGGAATGAGAGTAAAAGGATTTTGCCCACGGTCACGTGAGTAAACAACAGATTTGGAGGGGTCTGGACTACTGTGATGACTTCATTCTGACAATATGTTCCAGTTGTCCTTTCATTTCCTCCTAATCACATGTCTGGTCTGATCTGGCTGTTTCCCACCTTCCAATTCCTGCCTTCTCCAATGCTCCCT 0 false 0 sequence CACATG 0 false 0 sequence_with_flank TTTCCTCCTAATCACATGTCTGGTCTGATCTGGCTGTTTCC 0 false Homo sapiens OREG0000058 7391 USF1 NCBI TRANSCRIPTION FACTOR BINDING SITE Binding sequence was determined computationally as the canonical binding sequence. Only the AC sequence of the binding site was biologically tested. 30-Sep-2005 smontgom 30-Sep-2005 Addition of unlabelled CRE sequence in excess eliminated protein binding. When competed with mutant CRE sequence, the binding was not abolished tgGAttca (change from AC to GA) 30-Sep-2005 OREGEC00001 OREGES00003 OREGET00001 smontgom Antibodies to Jun family super shifted complex. 30-Sep-2005 OREGEC00002 OREGES00002 OREGET00001 smontgom tgGAttca (change from AC to GA) mutation reduced enhancer activity by 80% 30-Sep-2005 OREGEC00002 OREGES00004 OREGET00002 smontgom 1576 CYP3A4 NCBI 60 POSITIVE OUTCOME 14742674 0 search_space GTCGTTAGAATCTGAACTTCCTGAAGTTCATGTGCAAAGTTGAGTTAATTGTTTAATATTCAACAAGGATTATGCCAGTAAGATGGTAGGAAAATATTAGATATGTGTCATCACTGCTGGTATTATTTAAACTGCAACATATTTTAGCTGGCTGCTGATCTCAGCCACCATGCCTGCATTTTATCTCTGTCTCGTGGTCTGCAACCTTGGAAGCTTTGAACTTAGCTCATAGAATCCTGGGCATCAAGAACATGTGGTTCTAATGGCTAGATAGGGAATGAGAGTAAAAGGATTTTGCCCACGGTCACGTGAGTAAACAACAGATTTGGAGGGGTCTGGACTACTGTGATGACTTCATTCTGACAATATGTTCCAGTTGTCCTTTCATTTCCTCCTAATCACATGTCTGGTCTGATCTGGCTGTTTCCCACCTTCCAATTCCTGCCTTCTCCAATGCTCCCT 0 false 0 sequence TGACTTCA 0 false 0 sequence_with_flank TTTGGAGGGGTCTGGACTACTGTGATGACTTCATTCTGACAATATGTTCCAGTTGT 0 false Homo sapiens OREG0000059 AP1 (Jun family) CRE AP1 (Jun family) CRE USER DEFINED TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 smontgom ENSG00000092969 TGF-beta 2 (transforming growth factor b ENSEMBL homo_sapiens_core_32_35a 61 POSITIVE OUTCOME 15647279 0 sequence_with_flank EMPTY 0 false 0 sequence AGTTCAGATCCGCCACTCCGCACCCGAGACTGACACACTGAACTCCAC 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000060 REGULATORY REGION 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 smontgom ENSG00000092969 TGF-beta 2 (transforming growth factor b ENSEMBL homo_sapiens_core_32_35a 62 POSITIVE OUTCOME 15647279 0 sequence_with_flank EMPTY 0 false 0 sequence CAAGCAGGATACGTTTTTCTGTTGGGCATTGACTAGATTGTTTGCAAAAG 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000061 REGULATORY REGION 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 smontgom ENSG00000092969 TGF-beta 2 (transforming growth factor b ENSEMBL homo_sapiens_core_32_35a 63 POSITIVE OUTCOME 15647279 0 sequence_with_flank EMPTY 0 false 0 sequence ATTTTTTTCTTCTTACTCGCCAAAGTCAGGGTTC 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000062 REGULATORY REGION 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 smontgom ENSG00000092969 TGF-beta 2 (transforming growth factor b ENSEMBL homo_sapiens_core_32_35a 64 POSITIVE OUTCOME 15647279 0 sequence_with_flank EMPTY 0 false 0 sequence AATATTTCCACTTTTGGAACTACTGGCCTTTTCTTTTTAAAGGAATT 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000063 REGULATORY REGION 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 smontgom ENSG00000023287 RB1 ENSEMBL homo_sapiens_core_32_35a 65 POSITIVE OUTCOME 15618023 0 sequence_with_flank EMPTY 0 false 0 sequence GGCGGAAGT 0 false 0 sequence_with_flank ttccccacagacgccggcgggcccgggagcctcgcggacgtgacgccgcgGGCGGAAGTgacgttttcccgcggttggacgcggcgctcagttgccgggcg 0 false Homo sapiens OREG0000064 E4TF1, Fli-1 (RBF Motif) E4TF1, Fli-1 (RBF Motif) USER DEFINED TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 smontgom ENSG00000023287 RB1 ENSEMBL homo_sapiens_core_32_35a 66 POSITIVE OUTCOME 15618023 0 sequence_with_flank EMPTY 0 false 0 sequence CGGGCGG 0 false 0 sequence_with_flank agttccccacagacgccggcgggcccgggagcctcgcggacgtgacgccgCGGGCGGaagtgacgttttcccgcggttggacgcggcgctcagttgccggg 0 false Homo sapiens OREG0000065 ENSG00000185591 Sp1 ENSEMBL homo_sapiens_core_32_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 smontgom ENSG00000023287 RB1 ENSEMBL homo_sapiens_core_32_35a 67 POSITIVE OUTCOME 15618023 0 sequence_with_flank EMPTY 0 false 0 sequence CGGGCGGGGGA 0 false 0 sequence_with_flank ccgcgggcggaagtgacgttttcccgcggttggacgcggcgctcagttgcCGGGCGGGGGAgggcgcgtccggtttttctcaggggacgttgaaattattt 0 false Homo sapiens OREG0000066 ENSG00000185591 Sp1 ENSEMBL homo_sapiens_core_32_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 smontgom ENSG00000023287 RB1 ENSEMBL homo_sapiens_core_32_35a 68 POSITIVE OUTCOME 15618023 0 sequence_with_flank EMPTY 0 false 0 sequence GGAAGTGACG 0 false 0 sequence_with_flank cccacagacgccggcgggcccgggagcctcgcggacgtgacgccgcgggcGGAAGTGACGttttcccgcggttggacgcggcgctcagttgccgggcgggg 0 false Homo sapiens OREG0000067 ENSG00000141510 p53(TP53) ENSEMBL homo_sapiens_core_32_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 smontgom ENSG00000023287 RB1 ENSEMBL homo_sapiens_core_32_35a 69 POSITIVE OUTCOME 15618023 0 sequence_with_flank EMPTY 0 false 0 sequence GTGACGTTT 0 false 0 sequence_with_flank cagacgccggcgggcccgggagcctcgcggacgtgacgccgcgggcggaaGTGACGTTTtcccgcggttggacgcggcgctcagttgccgggcgggggagg 0 false Homo sapiens OREG0000068 ENSG00000115966 ATF-2 ENSEMBL homo_sapiens_core_32_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 smontgom ENSG00000023287 RB1 ENSEMBL homo_sapiens_core_32_35a 70 POSITIVE OUTCOME 15618023 0 sequence_with_flank EMPTY 0 false 0 sequence TTTCCCGC 0 false 0 sequence_with_flank cggcgggcccgggagcctcgcggacgtgacgccgcgggcggaagtgacgtTTTCCCGCggttggacgcggcgctcagttgccgggcgggggagggcgcgtc 0 false Homo sapiens OREG0000069 ENSG00000101412 E2F-1 (E2F1) ENSEMBL homo_sapiens_core_32_35a TRANSCRIPTION FACTOR BINDING SITE 16-Aug-2005 16-Aug-2005 OREGEC00000 OREGES00000 OREGET00000 smontgom ENSG00000023287 RB1 ENSEMBL homo_sapiens_core_32_35a 71 POSITIVE OUTCOME 15618023 0 sequence_with_flank EMPTY 0 false 0 sequence AGAGGACGGGGCGTGCCCCGACGTG 0 false 0 sequence_with_flank tccggtttttctcaggggacgttgaaattatttttgtaacgggagtcgggAGAGGACGGGGCGTGCCCCGACGTGcgcgcgcgtcgtcctccccggcgctc 0 false Homo sapiens OREG0000070 ENSG00000141510 p53(TP53) ENSEMBL homo_sapiens_core_32_35a TRANSCRIPTION FACTOR BINDING SITE Designated a low-penetrance allele by authors. 30-Sep-2005 smontgom 30-Sep-2005 The annotated variant allele has lower protein binding affinity (A allele). 30-Sep-2005 OREGEC00001 OREGES00001 OREGET00001 smontgom Cell-lines: MCF-7 and HepG2. In MCF-7, 1.9 fold higher expression for reference allele (G allele). In HepG2, this is 1.4 fold higher. (From 1999 study by same author) 30-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom 1576 CYP3A4 NCBI 72 POSITIVE OUTCOME 14673875 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000071 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 30-Sep-2005 0 reference_sequence agacaagggcaGgagagaggc 0 false rs2740574 dbSNP GERMLINE 0 variant_sequence agacaagggcaAgagagaggc 0 false The mutation is present in the canonical genome sequence it is A(T)10AT. 30-Sep-2005 smontgom Record represents a deletion. The variant sequence is present in hg18, while the reference sequence with a deletion represents that changed sequence. 26-Apr-2007 bcb 30-Sep-2005 Allele frequence in 87 Japanese (60%), 50 Caucasion (39%), and African-American (44%). The mutation is present in the canonical genome sequence it is A(T)10AT. 30-Sep-2005 OREGEC00000 OREGES00011 OREGET00006 smontgom Cell line: HepG2 (human hepatoblastoma). Variant allele A(T)10AT has 2.6-fold more activity than reference A(T)9AT allele. 30-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom 54600 UGT1A9 NCBI 73 POSITIVE OUTCOME 15115919 0 search_space CTCATATATTCTTGTTCTTTTGGGTAAATCATTGTCAGTGACTGATTTTTTTTTTATGAAAGGATAAAAACACGCCCTCTATTGGGGTCAGGTTTTGTGCTGGTATTTCTCCCACCTACTGTATCATAGGAGCTTAGATTCCCAGCTGCTTGCTCTCAGCTGCAGTTCTCTG 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000072 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 30-Sep-2005 0 reference_sequence tcattgtcagtgactgatttttttttatgaaaggataa 0 false rs3832043 dbSNP GERMLINE 0 variant_sequence tcattgtcagtgactgatttttttttTatgaaaggataa 0 false EMSA test was also performed but the annotated polymorphism did not alter binding of nuclear factors. 30-Sep-2005 smontgom 30-Sep-2005 In MC and C2C12 cell lines, activity with G allele was 1.4-fold higher than activity with C allele. 30-Sep-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom 2673 GFPT1 NCBI 74 NEUTRAL OUTCOME 15878746 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000073 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 30-Sep-2005 0 reference_sequence cttaatcatataaCcagccatagaa 0 false GERMLINE 0 variant_sequence cttaatcatataaGcagccatagaa 0 false Retested in 93 samples for serum resistin levels. G/G genotype had higher serum resistin levels than C/C. 30-Sep-2005 smontgom 30-Sep-2005 Nuclear proteins bound to the G allele but not to the C allele. A competitor to G when added in excess competed out binding. Cell line: 3T3-L1 adipocytes. 30-Sep-2005 OREGEC00001 OREGES00003 OREGET00001 smontgom Identified polymorphism by resequencing ~1kb upstream of 24 Japanese patients with T2DM (Type 2 Diabetes Mellitus). 30-Sep-2005 OREGEC00000 OREGES00010 OREGET00006 smontgom Antibodies to Sp1 weakly affected protein binding. Antibodies to Sp3 strongly affected protein binding. Together, the complex was entirely supershifted. 30-Sep-2005 OREGEC00002 OREGES00002 OREGET00001 smontgom 3-fold).]]> 30-Sep-2005 OREGEC00002 OREGES00004 OREGET00002 smontgom 56729 RETN NCBI 76 POSITIVE OUTCOME 15338456 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000075 Sp1 / Sp3 Sp1 / Sp3 USER DEFINED REGULATORY POLYMORPHISM 30-Sep-2005 0 reference_sequence ccttcccacttccaacagggcctccGtcttcatgtccagagactggtcagg 0 false rs1862513 dbSNP GERMLINE 0 variant_sequence ccttcccacttccaacagggcctccCtcttcatgtccagagactggtcagg 0 false The binding activity was constitutive as EMSA signal intensities not affected by clobetasol propionate or Terbutalin. AP-2 was tested in complex but was not the causal transcription factor for differential expression. 30-Sep-2005 smontgom 30-Sep-2005 17-18% reduction in transcription from the C allele as compared to the T allele 30-Sep-2005 OREGEC00000 OREGES00009 OREGET00004 smontgom One of the complexes shifted with the T allele was less abundant than a complex shifted with the C allele. 30-Sep-2005 OREGEC00000 OREGES00001 OREGET00001 smontgom 154 ADRB2 NCBI 77 POSITIVE OUTCOME 15578262 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000076 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 30-Sep-2005 0 reference_sequence ccgcccgggccagccCcaggagaaggaggg 0 false rs11959427 dbSNP GERMLINE 0 variant_sequence ccgcccgggccagccTcaggagaaggaggg 0 false Search space sequence is the targetted EMSA sequence. 1-Oct-2005 smontgom 1-Oct-2005 Cell lines: MDA-MB-231, MCF-7, HEK-293, and SL-2. SL-2 line is Sp-1 deficient; demonstrated ~100-fold induction when contransfected with Sp1; EGFR expression dependent on Sp1. Lower promoter activity observed with G allele compared to T allele. 1-Oct-2005 OREGEC00002 OREGES00004 OREGET00002 smontgom Cell line: MDA-MB-231. Affinity of nuclear proteins to T allele was higher than G allele. Assay with pure Sp1 demonstrated similar results. 1-Oct-2005 OREGEC00002 OREGES00001 OREGET00001 smontgom Cell type: Human fibroblast cells. EGFR mRNA (using 10 cell lines with diplotype G-C/T-C) was ~40% higher with T allele than G allele. (In vivo assay) 1-Oct-2005 OREGEC00001 OREGES00009 OREGET00004 smontgom 1956 EGFR NCBI 78 POSITIVE OUTCOME 15665278 0 search_space gcagcctccgccccccgcacggtgt 0 false 0 sequence cctccgcccc 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000087 6667 SP1 NCBI REGULATORY POLYMORPHISM 1-Oct-2005 0 reference_sequence ccgcagcagcctccGccccccgcacg 0 false rs712829 dbSNP GERMLINE 0 variant_sequence ccgcagcagcctccTccccccgcacg 0 false 1-Oct-2005 Protein bound with higher affinity to T allele than G allele and was competed out with excess unlabelled T-probe. 1-Oct-2005 OREGEC00001 OREGES00001 OREGET00001 smontgom Pre-incubation with antibody to Sp1 removed formation of complex. 1-Oct-2005 OREGEC00002 OREGES00001 OREGET00001 smontgom Cell line: Human myeloid leukaemia premonocyte cell line: THP-1. Comparison of promoter activity show greater activity with T allele than G allele (D compared with F haplotype in reference) 1-Oct-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom 6696 SPP1 NCBI 79 POSITIVE OUTCOME 16009426 0 search_space CATCTAGAATAAATTACCATTCTTCTATTTCATATAGAATTTTATATTTTAATGTCACTAGTGCCATTTGTCTAAGTAACAAGCTACTGCATACTCGAAATCACAAAGCTAAGCTTGAGTAGTAAAGGACAGAGGCAAGTTTTCTGAACTCCTTGCAGGCTTGAACAATAGCCTTCTGGCTCTTCAATAAGTACAATCATACAGGCAAGAGTGGTTGCAGATATTACCTTTATGTTACTTAAACCGAAAGAAACAAAAATCCATTCTATTTAATTTTACATTAATGTTTTTCCCTACTTTCTCCCTTTTTCATGGGATCCCTAAGTGCTCTTCCTGGATGCTGAATGCCCATCCCGTAAATGAAAAAGCTAGTTAATGATATTGTACATAAGTAATGTTTTAACTGTAGATTGTGTGTGTGCGTTTTTGTTTTTTTTTGTTTTAACCACAAAACCAGAGGGGGAAGTGTGGGAGCAGGTGGGCTGGGCAGTGGCAGAAAACCTCATGACACAATCTCTCCGCCTCCCTGTGTTGGTGGAGGATGTCTGCAGCAGCATTTAAATTCTGGGAGGGCTTGGTTGTCAGCAGCAGCAGGAGGAGGCAGAGCACAGCATCGTCGGGACCAGACTCGTCTCAGGCCAGTTGCAGCCTTCTCAGCCAAACGCCGACCAAGGTACAGCTTCAGTTTGCTACTGGGTTGTGCAT 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000088 6667 SP1 NCBI REGULATORY POLYMORPHISM 1-Oct-2005 0 reference_sequence atgacacaatctcTccgcctccctgtg 0 false GERMLINE 0 variant_sequence atgacacaatctcGccgcctccctgtg 0 false Association studies performed. 1-Oct-2005 smontgom 1-Oct-2005 Cell line: COS-1 cells. A allele demonstrated two-fold decrease in promoter activity compared to C allele. 1-Oct-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom Mutant allele (A) showed little or no binding to (mouse) liver nuclear proteins and separately, weakly bound purified TFIID. C allele showed binding of both liver nuclear proteins and purified TFIID (separately) 1-Oct-2005 OREGEC00002 OREGES00001 OREGET00001 smontgom 350 APOH NCBI 80 POSITIVE OUTCOME 12605674 0 search_space CCAAGACATATTAAGAATGGATGAGGAGGACTTTGTATTGATCTGACGTAAGAGAAGATAGAGAATTCAAGGATAGCTCTAAGGTCCTAACTGGAGCTATAGGAGCTTGCAAGAGAGGATGTTGAGCTCAGTTTGTAGGGAATTAAAGTTGTAAGTGCCTCCTGGAAGACATTCTTTGTAATTATACATCTGAAAACTGGAACATCATTTTAGAGAGGTGGAGACTGAGAACAGAGAGTAGGTGTTTGTCCAAAGTTTATATGCCAAGGCTGTGAGTGAAACAGGAGCTTCGATCTTTTGGTGTTCCATCTACAACATACACAAAACAAAAGATGGAGAATGAGAAGTCCAGGCAACCCCGGAAACAACAAGTTTCTGTCAAAAGCAATAATGAACTGTTTTGTGCCATTAACAAAAACGTTATGAAGACAGAAACCATCTCCCAAAGATTTCATAACAGAGCCACATAAGTGGAAAGTAAATGATTAAAGAATGTGGGTCTCAGAGTTCCATTCAAATCATGATACTTTATCTTCTATTTACAAAGATAAAAGTACACCAGAAAATGGTTAATGTTTAAGCGCTTTCATATTTGGCTCTGTCTTTTTAGCAGACGAAAACCACTTTGGTAGTGCCAGTGTGACTCATCCACAATGATTTCTCCAGTGCTCATCTTGTTCTCGAGTTTTCTCTGCC 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000089 TFIID TFIID USER DEFINED REGULATORY POLYMORPHISM 1-Oct-2005 0 reference_sequence ctgtctttttagcagacgaaaacCactttggtagtgccagtgt 0 false rs8178822 dbSNP GERMLINE 0 variant_sequence ctgtctttttagcagacgaaaacAactttggtagtgccagtgt 0 false Polymorphism identified to increase transcription of CD14 by lowering the affinity of the CD14 regulatory region for Sp3 (inhibitory factor). 1-Oct-2005 smontgom 1-Oct-2005 Cell line: Mono Mac 6 cells. C allele had strong basal transcription activity. T allele resulted in 32% increase in gene expression 1-Oct-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom Tested Sp and AP2 oligonucleotides. Sp family oligonucleotides competed out binding. Similar results with HeLa nuclear extracts (competed out by Sp family oligonucleotides). Mutation tests showed polymorphism affected affinity for Sp family binding. 1-Oct-2005 OREGEC00002 OREGES00003 OREGET00001 smontgom Tested with antibodies to Sp1, Sp2, and Sp3 successfully. 1-Oct-2005 OREGEC00002 OREGES00002 OREGET00001 smontgom 929 CD14 NCBI 81 POSITIVE OUTCOME 11698458 0 search_space GGCGCCTGAGTCATCAGGACACTGCCAGGAGACACAGAACCCTAGATGCCCTGCAGAATCCTTCCTGTTACGGTCCCCCTCCCTGAAACATCCTTCATTGCAATATTTCCAGGAAAGGAAGGGGGCTGGCTCGGAGGAAGAGAGGTGGGGAGGTGATCAGGGTTCACAGAGGAGGGAACTGAATGACATCCCAGGATTACATAAACTGTCAGAGGCAGCCGAAGAGTTCACAAGTGTGAAGCCTGGAAGCCGGCGGGTGCCGCTGTGTAGGAAAGAAGCTAAAGCACTTCCAGAGCCTGTCCGG 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000090 Sp1 / Sp2 / Sp3 (Sp family) Sp1 / Sp2 / Sp3 (Sp family) USER DEFINED REGULATORY POLYMORPHISM 1-Oct-2005 0 reference_sequence cttcctgttacggTccccctccctgaaacatc 0 false rs2569190 dbSNP GERMLINE 0 variant_sequence cttcctgttacggCccccctccctgaaacatc 0 false 2-Oct-2005 Leptin serum levels 50% higher than in AA than GA/GG genotypes. Two-fold increase in adipose tissue leptin secretion by AA vs GA/GG subjects. Population: 39 healthy female swedish subjects (10 GG, 18 GA, 11 AA) 2-Oct-2005 OREGEC00000 OREGES00010 OREGET00006 smontgom Cell line: U937 and subcutaneous adipocytes. Nuclear factors bound with higher affinity to A allele. Probe used is annotated as search space sequence. One protein complex formed in U937 cells as opposed to two in human adipose tissue. 2-Oct-2005 OREGEC00001 OREGES00001 OREGET00001 smontgom 3952 LEP NCBI 82 POSITIVE OUTCOME 12189581 0 search_space GCGACAGGGTTGCGCTGATCCTCC 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000091 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 2-Oct-2005 0 reference_sequence tattcttcttttgttttgttttgcgacagggttgcGctgatcctcccgcctc 0 false rs7799039 dbSNP GERMLINE 0 variant_sequence tattcttcttttgttttgttttgcgacagggttgcActgatcctcccgcctc 0 false Flow cytometry showed a higher expression of human alpha-chain on plasmid carrying T allele. 2-Oct-2005 smontgom 2-Oct-2005 Cell line: PT18, and RBL-2H3. Luciferase activity higher from T allele than C allele (construct annotated as search space sequence). Similar results observed in KU812 cell line. 2-Oct-2005 OREGEC00000 OREGES00004 OREGET00002 smontgom Performed with overproduced GATA-1. T allele activity was ~4-fold higher than C allele (increased only 2-fold from previous assay). T allele responded better to GATA-1. 2-Oct-2005 OREGEC00002 OREGES00004 OREGET00002 smontgom Tested specific binding for GATA-1. GATA-1 bound T allele at lower potential than canonical binding sequence. Had two times greater affinity than C allele for GATA-1. 2-Oct-2005 OREGEC00002 OREGES00001 OREGET00001 smontgom Resequenced 54 Japanese individuals. 96.2% of patients with atopic dermititis had T/T/ genotype 2-Oct-2005 OREGEC00000 OREGES00010 OREGET00006 smontgom 2205 FCER1A NCBI 83 POSITIVE OUTCOME 12902495 0 search_space GCTAGCCATGCTCCTGAATATGTATAAACAGTACATCATATGACTAAGAGTTTGACTTAGGGGTTAGATTTTATGTGTTTGAACCCCAAATTAGTTATTTAATAGTTGGCACCCCAAAACAAGTTACTTAACCTCACTAAGATTCAGTTTTCCTGTTTATAAAATGTAGATAGTGATAGTATGTACTTTATAGGATTATTGTGAAAAATAAATGAAATATCAGATTTATTTAGGATAACACCTGGCATATGTTTGGTATTCAGTAATTAGTTGCTGCTGTTTTATTCTGCTCTCCCTTGCATCCCACTTTTCTAAGTTGTAAACTAAATAGTTGTACACAGATTGACAGATTAAGAAAGGCTTGTGATTGTGCTAGACCTATGCCTCTCTCTCACCAGATTCCAGGTGTATATGTGGAGGTGGGATAGGGAGTGGAGTAAGTGGGTAAATATTAAATTGCCCAGTTGGGCACCATCCTGAATATTATCTCTAAAGAAAGAAGCAAAACCAGGCACAGCTGATGGGTTAACCAGATATGATACAGAAAACATTTCCTTCTGCTTTTTGGTTTTAAGCCTATATTTGAAGCCTTAGATCTCTCCAGCACAGTAAGCACCAGGAGTCCATGAAGAAGA 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000092 2623 GATA1 NCBI REGULATORY POLYMORPHISM 2-Oct-2005 0 reference_sequence agctgatgggttaaccagatatgaTacagaaaacattt 0 false rs2251746 dbSNP GERMLINE 0 variant_sequence agctgatgggttaaccagatatgaCacagaaaacattt 0 false Authors noted variant causes new CCAAT box in mutant sequence. Mutation detected from 2 Chinese Type 2 diabetes mellitus patients. 2-Oct-2005 smontgom 2-Oct-2005 HeLa cells transfected. C allele had higher activity (15.7% +/- 4.1%) than A allele (5.7% +/- 2.9%). Used B-Gal assay. 2-Oct-2005 OREGEC00001 OREGES00004 OREGET00002 smontgom T had slower shift mobility that WT C allele. Authors suggested role as possible repressor. 2-Oct-2005 OREGEC00001 OREGES00001 OREGET00001 smontgom 231 AKR1B1 NCBI 84 POSITIVE OUTCOME 14515207 0 search_space CGCTAAAGCATTCGCTTTCCCACCAGATACAGCAGCTGAGGAACTCCTTTCTGCCACGCGGGGCGCGGGCGAGCGTTGGGGGCGGAAAGAATCCGCTGCCACTAGGACCAGGCGGAAGAAGCATCCCCGCCGACCCTTGGGGAAGGCCGCCGCGGCACCCCCAGCGCAACCAATCAGAAGGCTCCTTCGCGCAGCGGCGCGCCAACCGCAGGCGCCCTTTCTGCCGACCTCACGGGCTATTTAAAGGTACGCGCCGCGGCCAAGGCCGCACCGTACTGGGCGGGGGTCTGGGGAGCGCAGCAGCCAT 0 false 0 sequence_with_flank EMPTY 0 false 0 sequence_with_flank EMPTY 0 false Homo sapiens OREG0000093 UNKNOWN UNKNOWN USER DEFINED REGULATORY POLYMORPHISM 2-Oct-2005 0 reference_sequence cggaaagaatccgctgccaCtaggaccaggcggaaga 0 false GERMLINE 0 variant_sequence cggaaagaatccgctgccaAtaggaccaggcggaaga 0 false 2-Oct-2005 Cell lines: Calu-3, CF-PAC1, and HeLa. A allele had increased promoter activity by 60%, 66%, and 45% in the respective cell types. 2-Oct-2005 OREGEC00000 OREGES00004 OREGET00002 smontgom Oligonucleotides assayed harboring various cis-acting consensus sequences. Minimal promoter may act with SRF-like protein. 2-Oct-2005 OREGEC00002 OREGES00001 OREGET00001 smontgom Tested SRF-1 and YY1 protein. Factors could both occupy variant binding region. 2-Oct-2005 OREGEC00002 OREGES00003 OREGET00001 smontgom Supershift against tr