Position from | Position in Refseqa | dbSNP | Sequence | Region | AF in | Effect on mRNA Expressionb and TRANSFAC Change | Region | Tag SNP | ||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
TSS | ATG | PDR44 | Whites | Hispanics | African Americans | |||||||
Numbering based on AC097484 | ||||||||||||
-79753 | -98670 | 145770 | rs1114568 | tcact[a/g]atgct | Upstream | |||||||
-71762 | -90679 | 137779 | tcatg[t/a]gttca | Upstream | 0.04 | N.A. | N.A. | N.A. | I | |||
-71813 | -90730 | 137830 | caaaa[a/g]tgcaa | Upstream | 0.06 | N.A. | N.A. | N.A. | I | |||
-71997 | -90914 | 138014 | rs10032109 | tgaca[c/t]atttg | Upstream | 0.06 | N.A. | N.A. | N.A. | I | ||
-71961 | -90878 | 137978 | atatg[c/t]aagtt | Upstream | 0.04 | N.A. | N.A. | N.A. | I | |||
-72258 | -91175 | 138275 | ttggg[g/a]cagga | Upstream | 0.12 | N.A. | N.A. | N.A. | I | |||
-69504 | -88421 | 135521 | rs9307048 | cagacc[c/t]gggat | Upstream | |||||||
-30639 | -49556 | 96656 | aataa[-ataa]gaaat | Upstream | 0.28 | 0.27 | 0.30 | 0.41 | Decreased mRNA (L); loss of 1Hnf1 site | II | ||
-30562 | -49479 | 96579 | rs2127862 | gccac[t/c]gtact | Upstream | 0.70 | 0.47 | 0.59 | 0.26 | II | ||
-30477 | -49394 | 96494 | rs2127861 | tgctt[c/g]tattc | Upstream | 0.94 | 0.80 | 0.82 | 0.85 | Decreased mRNA (L) | II | |
-30109 | -49026 | 96126 | acaac[ins-a]aaaaa | Upstream | 0.70 | 0.50 | 0.54 | 0.35 | II | |||
Numbering based on AC084732 | ||||||||||||
-17824 | -36741 | 2535 | rs13135956 | caagg[c/t]gagag | Upstream | 0.19 | 0.23 | 0.09 | 0.47 | III | ||
-17750 | -36667 | 2609 | rs13111149 | aaaaa[a/g]aaaaa | Upstream | 0.19 | 0.23 | 0.09 | 0.44 | III | ||
-17243 | -36160 | 3116 | rs1481016 | aaaaa[a/c]tgaga | Upstream | 0.16 | 0.27 | 0.14 | 0.59 | III | ||
-17242 | -36159 | 3117 | aaaaa[t/c]gagaa | Upstream | 0.56 | 0.63 | 0.55 | 0.76 | III | |||
-17084 | -36001 | 3275 | rs1481014 | tggag[g/a]attgg | Upstream | 0.00 | 0.23 | 0.14 | 0.38 | III | YRI | |
-15994 | -34911 | 4365 | rs7699188 | tacac[c/t]ttata | Upstream | 0.22 | 0.07 | 0.09 | 0.06 | Increased mRNA (L,I,P); gain of 1HNF4 site | III | |
-15846 | -34763 | 4513 | gcaac[a/c]aaagc | Upstream | 0.09 | 0.07 | 0.13 | 0.06 | Increased mRNA (L,I,P) | III | ||
-15756 | -34673 | 4603 | ctcac[g/a]cctgt | Upstream | 0.22 | 0.07 | 0.14 | 0.03 | III | |||
-15672 | -34589 | 4687 | tggag[a/g]aaccc | Upstream | 0.21 | III | ||||||
-15622 | -34539 | 4736 | ggtgg[c/t]gcatg | Upstream | 0.20 | 0.03 | 0.14 | 0.06 | Decreased mRNA (L,I,P) | III | ||
-13680 | -32597 | 6679 | aatta[-a]ttttt | Upstream | 0.07 | 0.07 | 0.05 | 0.06 | Loss 2LHX3, gain 1FoxD3 | IV | ||
-13000 | -31917 | 7924-8055 | ?insertion | Upstream | hets not known | hets not known | hets not known | hets not known | V | |||
-13359 | -32276 | 7345 | tagca[c/t]actgt | Upstream | 0.01 | V | ||||||
-12968 | -31885 | 7391 | gcttc[g/a]acctt | Upstream | 0.14 | V | ||||||
-12945 | -31862 | 7414 | gatta[c/g]aggca | Upstream | 0.08 | V | ||||||
-12870 | -31787 | 7489 | aggtg[t/a]cttaa | Upstream | 0.02 | Gain of 1 AP1 site | V | |||||
-11868 | -30785 | 8491 | gagcc[g/a]gtcgc | Upstream | 0.01 | V | ||||||
-6055 | -24972 | 14304 | rs11383890 | acccc[+c]atctc | Upstream | 0.59 | 0.57 | 0.55 | 0.62 | VI | ||
-6219 | -25136 | 14485 | acaaa[a/c]aacaa | Upstream | 0.02 | VI | ||||||
-5267 | -24184 | 15092 | rs2725226 | tgagg[t/c]agtag | Upstream | 0.57 | 0.57 | 0.55 | 0.62 | VI | ||
-5113 | -24030 | 15246 | ctttt[-t]aaaaa | Upstream | 0.07 | VI | ||||||
-3602 | -22519 | 16757 | rs3114020 | tccca[g/a]tgtaa | Upstream | 0.59 | 0.57 | 0.55 | 0.62 | VII | YRI | |
-3335 | -22252 | 17024 | rs6846742 | acatt[c/g]catgt | Upstream | 0.01 | VII | |||||
-3243 | -22160 | 17116 | ggctc[g/a]ctgca | Upstream | 0.07 | VII | ||||||
-2959 | -21876 | 17400 | tcaca[c/g]cagtt | Upstream | 0.06 | VII | ||||||
-2728 | -21645 | 17631 | acaca[g/t]gcaca | Upstream | 0.59 | 0.57 | 0.55 | 0.62 | VII | |||
-790 | -19707 | 19705 | rs4148162 | cactca[-ctca]caaag | Upstream | 0.59 | 0.57 | 0.55 | 0.62 | VIII | ||
-212 | -19129 | 20147 | gcggg[+g]agtgt | Upstream | 0.06 | 0.03 | 0.05 | 0.00 | VIII | |||
681 | -18236 | 21040 | rs2622605 | tatgc[g/t]gttta | Intron 1 | 0.57 | 0.50 | 0.55 | 0.50 | VIII | CHB | |
1143 | 17774 | 21502 | rs2622604 | aatac[g/a]ccaga | Intron 1 | 0.15 | 0.33 | 0.29 | 0.15 | Decreased mRNA (L,I,P) | VIII | CEU |
1450 | -17467 | 21809 | ataac[a/c]tgggc | Intron 1 | 0.04 | 0.17 | 0.00 | 0.00 | VIII | |||
6861 | -12056 | 27220 | rs9999111 | tgaat[t/c]cacag | Intron 1 | 0.09 | IX | |||||
7250 | -11667 | 27609 | ttcac[g/t]ccatt | Intron 1 | 0.26 | IX | ||||||
7438 | -11479 | 27797 | agcca[c/a]tgcac | Intron 1 | 0.08 | IX | ||||||
9496 | -9421 | 29855 | tctcc[g/a]ttccc | Intron 1 | 0.01 | Loss 1CDX, 1Hnf1, gain 1Hnf3 | X | |||||
9666 | -9251 | 30025 | tcttt[t/g]attta | Intron 1 | 0.06 | 0.00 | 0.02 | 0.00 | X | |||
9908 | -9009 | 30267 | atgaa[a/g]aaaca | Intron 1 | 0.01 | X | ||||||
9932 | -8985 | 30291 | gtctt[a/c]tgttc | Intron 1 | 0.01 | X | ||||||
11560 | -7357 | 31919 | rs2725246 | taaag[t/c]tgtta | Intron 1 | 0.54 | XI | |||||
11603 | -7314 | 31962 | rs17731799 | aggta[a/c]gtttt | Intron 1 | 0.44 | XI | CEU | ||||
12283 | -6634 | 32642 | tgagg[t/c]tggga | Intron 1 | 0.06 | 0.00 | 0.04 | 0.07 | Increased mRNA (L,P) | XI | ||
12638 | -6279 | 32997 | rs11287117 | aggaa[-c]ccagc | Intron 1 | 0.33 | XI | |||||
12674 | -6243 | 33033 | aagga[-t]ttttt | Intron 1 | 0.24 | XI | I | |||||
13070 | -5847 | 33429 | rs10632140 | ctgcc[-tcagc]gtccc | Intron 1 | 0.37 | XI | |||||
13989 | -4928 | 34348 | rs6857600 | gttgc[g/a]caatt | Intron 1 | 0.29 | 0.32 | 0.20 | 0.53 | Loss of 1 CEBPδ site | XII | |
15463 | -3454 | 35822 | rs3109823 | tttcc[a/g]tcttg | Intron 1 | 0.28 | 0.27 | 0.29 | 0.71 | XII | ||
15484 | -3433 | 35843 | rs3114018 | ctatt[g/t]aaatt | Intron 1 | 0.49 | 0.63 | 0.50 | 0.74 | XII | CEU YRI | |
16080 | -2837 | 36439 | rs2725250 | gtagc[t/c]gaaac | Intron 1 | 0.28 | 0.32 | 0.43 | 0.21 | XII | ||
16214 | -2703 | 36573 | rs2622620 | aaagt[t/g]ctggg | Intron 1 | 0.52 | 0.57 | 0.57 | 0.85 | XII | ||
16702 | -2215 | 37061 | rs2046134 | ttttg[c/t]tgcat | Intron 1 | 0.10 | 0.59 | 0.05 | 0.00 | Increased mRNA (L); gain of 1 GATA4 site | XII | YRI |
16711 | -2206 | 37070 | atttt[c/t]ccttc | Intron 1 | 0.04 | XII | ||||||
16823 | -2094 | 37182 | rs5860120 | ttttt[-t]ccccc | Intron 1 | 0.24 | 0.03 | 0.04 | 0.00 | Decreased mRNA (L) | XII | |
18951 | 34 | 39310 | rs2231137 | tccca[g/a]tgtca | Exon2 | 0.13 | 0.06 | 0.20 | 0.06 | Exon2 | ||
19156 | 239 | 39515 | rs4148152 | tttta[a/g]tttac | Intron 2 | 0.13 | 0.06 | 0.20 | 0.06 | |||
24353 | 5436 | 44712 | ttagg[g/c]agctg | Intron 2 | 0.01 | Intron2 | ||||||
24487 | 5570 | 44846 | tagat[c/t]ttgct | Intron 2 | 0.01 | Intron2 | ||||||
24580 | 5663 | 44939 | rs2725255 | ttcac[c/t]cttgt | Intron 2 | 0.05 | Intron2 | |||||
24686 | 5769 | 45045 | rs17731538 | tcact[c/t]ataat | Intron 2 | 0.12 | Intron2 | |||||
25049 | 6132 | 45408 | cccac[c/t]accgt | Intron 2 | 0.02 | Intron2 | ||||||
25398 | 6481 | 45757 | rs4148155 | cttca[t/c]attct | Intron 2 | 0.09 | 0.10 | 0.21 | 0.00 | Intron2 | CHB | |
25579 | 6662 | 45938 | rs17013859 | ctgaa[g/a]tgctt | Intron 2 | 0.11 | 0.00 | 0.14 | 0.12 | Intron2 | ||
26347 | 7430 | 46706 | rs2231138 | gtata[a/g]gagag | Intron 2 | 0.06 | Intron3 | |||||
27742 | 8825 | 48101 | rs2231142 | actta[c/a]agttc | Exon 5 | 0.12 | Exon5 | |||||
40981 | 22064 | 61340 | rs1481012 | ccagc[t/c]tgtta | Intron 7 | 0.13 | 0.00 | 0.13 | 0.07 | Intron 7 | CHB | |
50510 | 31593 | 70869 | rs2622628 | caaga[g/t]tggtg | Intron 9 | 0.19 | 0.10 | 0.18 | 0.21 | Intron 9 | ||
50987 | 32070 | 71346 | rs2054576 | tttgc[t/c]acata | Intron 9 | 0.14 | Intron 9 | |||||
51218 | 32301 | 71577 | agcca[t/g]tgagt | Intron 9 | 0.04 | Intron 9 | ||||||
51284 | 32367 | 71643 | rs2231148 | tgtgt[a/t]taagt | Intron 9 | 0.24 | Intron 9 | CEU | ||||
51493 | 32576 | 71852 | rs2231150 | tccat[t/g]aagaa | Intron 10 | 0.01 | Intron 10 | |||||
51526 | 32609 | 71885 | tgtaa[a/c]tgtca | Intron 10 | 0.02 | Intron 10 | ||||||
51538 | 32621 | 71897 | rs2231151 | tcttt[t/c]attga | Intron 10 | 0.01 | Intron 10 | |||||
51922 | 33005 | 72281 | rs7681519 | accat[c/g]caact | Intron 10 | 0.20 | Intron 10 | |||||
62989 | 44072 | 83348 | rs2231162 | tgact[c/t]ttagt | Intron 13 | 0.22 | Intron 13 | |||||
63217 | 44300 | 83576 | aactc[c/t]ctttt | Intron 14 | 0.01 | Intron 14 | ||||||
63596 | 44679 | 83955 | rs2725267 | aagaa[t/c]gaaag | Intron 14 | 0.28 | 0.10 | 0.29 | 0.74 | Intron 14 | ||
63914 | 44997 | 84273 | rs2231164 | ttctt[a/g]aaatt | Intron 14 | 0.43 | 0.06 | 0.30 | 0.68 | Intron 14 | CHB | |
64152 | 45235 | 84511 | rs2231165 | ttttc[c/t]gagcc | Intron 15 | 0.07 | Intron 15 | |||||
64681 | 45673 | 84949 | aaggc[c/t]gcata | Intron 15 | 0.39 | Intron 15 | ||||||
64984 | 45691 | 84967 | rs4148159 | gttgt[t/a]gtttt | Intron 15 | 0.04 | Intron 15 | |||||
64590 | 45764 | 85040 | rs4148160 | aataa[g/a]ttgag | Intron 15 | 0.01 | Intron 15 | |||||
64608 | 46067 | 85343 | tggtc[a/g]ggatg | Intron 15 | 0.12 | Intron 15 |
AF, allele frequency; CEU, Utah residents with ancestry from northern and western Europe; CHB, Han Chinese in Beijing, China; hets, heterozygotes; N.A., not applicable; YRI, Yoruba in Ibadan, Nigeria.
↵ a RefSeq = AC097484 or AC084732.
↵ b Effect of variant allele on mRNA expression in liver (L), PDR44 (P), and intestine (I).