TABLE 4

Polymorphisms identified in the ABCB11 gene

Numbering of nucleotides is according to the GenBank accession numbers AC008177.3 (promoter and exons 1–21) and AC069165.2 (newer classification AC069137.6) (exons 22–28). Positions of polymorphisms are counted with respect to the BSEP translation start (Exon 2) with the A of the start ATG being +1 and the 5′-following base being –1. The numbers 1 to 53 in the variant ID column indicate all variants included in haplotype analysis and linkage disequilibrium estimation.

Variant ID
5′ Sequence
Genetic Variation
3′ Sequence
Region
Amino Acid Change
CA
AA
JA
Total
n
 %
n
 %
n
 %
n
 %
54 GTAGTCACA g.-15595C>T TTTCAGAGC Promoter 186 0.5 92 0.0 88 0.0 366 0.3
1 ACACTCTCT g.-15281_-15278 delCTCT CACACAGCA Promoter 186 10.2 92 4.3 86 26.7 364 12.6
2 CCCCCTCCC g.-15150T>C GCCCCCAGA Promoter 148 48.0 76 39.5 92 25.0 316 58.9
3 TGACTGTAG g.-15018G>A GACCACAAC Promoter 158 10.1 78 0.0 92 29.3 328 13.1
4 ATTAAGCAC g.-14944G>A ATCAACTCA Promoter 198 10.1 72 0.0 96 28.1 366 12.8
5 CTATTGGGA g.-14589A>T TCTTTTCCC Promoter 198 0.0 90 2.2 88 0.0 376 0.5
55 TGAAGCAAA g.-14524A>T TTTTTTTCC Promoter 198 0.0 90 1.1 88 0.0 376 0.3
6 TACATTTGC g.-14473G>A TCAACTCAG Promoter 198 2.5 90 18.9 88 0.0 376 8.8
7 TTGCATAGA g.-14437G>A GAAACATCT Promoter 198 29.8 94 22.3 96 14.6 388 24.2
8 ATTATATGT g.-14353T>C ATAATTTTG Promoter 190 61.6 80 92.5 88 75.0 358 71.8
56 ATAAACCAT g.-14316C>A TTATACATA Promoter 192 0.5 80 0.0 88 0.0 360 0.3
9 ACCATCTTA g.-14312T>C ACATAAATT Promoter 192 0.0 80 0.0 88 3.4 360 0.8
57 ATAAATTCC g.-14300A>T ATAGAGAAA Promoter 192 0.0 80 1.3 88 0.0 360 0.3
10 TTTAATTTC g.-14207T>C GCAAATTAA Promoter 190 2.1 80 17.5 88 10.2 358 7.5
11 TTGTTACAC g.-14104C>T TTAGGAGGA Promoter 196 2.6 92 0.0 96 0.0 384 1.3
12 CATGATAGC g.-14035A>G CCCAACTCC Promoter 194 1.5 92 1.1 96 0.0 382 1.0
58 AAGGCTGGA g.-13910G>A TGAGAGGCA Promoter 202 0.0 94 1.1 96 0.0 392 0.3
13 AGAGGAAGA g.-13814G>A GCAGCACAA Promoter 194 0.0 94 6.4 88 0.0 376 1.6
14 GCACAAATA g.-13801T>C ATTGGAGCT Promoter 194 1.5 94 0.0 88 0.0 376 0.8
15 CTCAGACTT g.-13662T>C TGAGCAAGG Promoter 192 0.0 94 7.4 86 0.0 372 1.9
83 TTAAAGGTA g.-13523[T]9 GTCTTGTTA Promoter 200 10.0 90 11.1 96 28.1 386 14.8
84 TTAAAGGTA g.-13523[T]10 GTCTTGTTA Promoter 200 9.0 90 18.9 96 6.3 386 10.6
85 TTAAAGGTA g.-13523[T]11 GTCTTGTTA Promoter 200 65.0 90 53.3 96 45.8 386 57.5
86 TTAAAGGTA g.-13523[T]12 GTCTTGTTA Promoter 200 16.0 90 16.7 96 19.8 386 17.1
59 CTGGGCCAG g.-13595G>A AGCATCTGG Promoter 198 0.0 94 1.1 96 0.0 388 0.3
16 CAAGCACAC g.-1333T>C CTGTGTTTG Promoter 196 0.0 76 0.0 96 3.9 368 0.9
17 ATGTTTCTC g.-13297G>A TATGTCACT Promoter 196 0.0 76 3.9 96 0.0 368 0.8
60 TCCACAGTG g.-13142G>A AGTCCATTA Exon 1 194 0.0 76 0.0 92 1.1 362 0.3
18 TTGATTAAA g.-77G>A AAGAAAGAA Intron 1 202 2.5 88 11.4 90 12.2 380 6.8
19 ATTTTTTTT g.1319delT CTGACAGAT Intron 2 198 0.0 88 3.4 92 0.0 378 0.8
20 TTTAAATCC g.3754T>C TATGTTTTT Intron 3 198 7.1 62 32.3 88 12.5 348 12.9
21 GTTACAAGA g.3781T>C GAGAAGAAA Exon 4 D36D 198 0.0 62 0.0 88 26.1 348 6.6
22 GAATCTAGT g.4542A>T ACTAAATTA Intron 4 184 0.0 90 0.0 92 2.2 366 0.5
61 CAAGTTTCG g.4621G>A TTTTCTTCA Exon 5 R52R 184 0.0 90 1.1 92 0.0 366 0.3
23 AGATGTTTT g.4735T>C ATTGACTAC Exon 5 F90F 184 2.7 90 13.3 92 12.0 366 7.7
24 GGGTAGGTT g.4862G>A TTTTTGTTT Intron 5 182 4.9 90 2.2 94 0.0 366 3.0
25 GCTGAACAT g.21416C>T GAGAGCGAA Exon 6 I1341 192 0.0 86 18.6 88 0.0 366 4.4
26 AGCTCCTCC g.21507G>A TATAATTTA Intron 6 196 0.0 92 18.5 92 0.0 380 4.5
27 ACAATGAGA g.21554T>G GCAATGTGT Intron 6 196 0.0 92 0.0 92 4.3 380 1.1
62 TGTATTGAA g.22567A>T GTACTTTCT Intron 6 198 0.5 94 0.0 94 0.0 386 0.3
63 TTTGAATGA g.24203T>C CAAATTCAG Intron 7 192 0.5 90 0.0 94 0.0 376 0.3
64 TCTAGTGAT g.24248A>G TTAATAAAA Exon 8 I206V 194 0.0 90 1.1 96 0.0 380 0.3
28 TACGGACTA g.27224T>C GAGCTGAAG Exon 9 Y269Y 200 0.0 80 0.0 96 27.1 376 6.9
65 CTGATGAAG g.27268T>C CATTTCATC Exon 9 V284A 200 0.5 80 0.0 96 0.0 376 0.3
66 GTGAGAAAA g.27313G>A AGAGGTTGA Exon 9 R299K 200 0.0 80 0.0 96 1.0 376 0.3
29 ACTGCATCA g.31773C>T GGCCTGTTT Intron 9 178 5.1 70 1.4 48 0.0 296 3.4
30 TGTTTCTGC g.31811C>T GAAATTGAC Intron 9 196 4.6 72 4.2 86 0.0 354 3.4
31 TTGACTCAA g.31825G>A CATTTTGTC Intron 9 196 4.6 72 26.4 86 0.0 354 7.9
32 GACTCAAGC g.31827A>G TTTTGTCTT Intron 9 196 70.4 72 84.7 86 90.7 354 78.2
33 TAGAAAAGG g.31890A>G ATAGTGATG Exon 10 G319G 196 4.6 72 26.4 86 0.0 354 7.9
34 GACTTATTG g.32034A>T CCGAGACAT Intron 10 196 0.0 66 4.5 82 0.0 344 0.9
67 CCTCAGTGT g.38161C>T ATAGTAGGA Exon 11 V366V 196 0.0 88 1.1 94 0.0 378 0.3
35 CATTTTTGA g.38248G>A ACAATAGAC Exon 11 E395E 196 0.0 88 8.0 96 0.0 380 1.8
36 GCAGAGATA g.41348C>T GCCAAAGAT Intron 11 198 0.0 72 2.8 80 0.0 350 0.6
37 CCACAAATT g.41622G>T CTCATTTTC Intron 12 196 1.0 72 0.0 74 0.0 342 0.6
38 CAGTGACAA g.44255delT CTGAACTTT Intron 12 190 0.0 94 2.1 92 0.0 376 0.5
39 TCAACATGG g.44308T>C CATTAAACC Exon 13 V444A 190 59.5 90 65.6 92 80.4 372 66.1
40 TTGATCAAA g.44481C>T AGAAAGGTG Intron 13 188 59.0 90 65.6 92 80.4 370 65.9
68 CAAGGAGGC g.46246C>T AATGCCTAC Exon 14 A535A 184 0.0 86 0.0 96 1.0 366 0.3
41 GGGAGAAAC g.46311T>C AAGAGGTCG Intron 14 182 60.4 86 66.3 94 79.8 362 66.9
42 GTTGCTCAT g.48611C>G GCTTGTCTA Exon 16 R616G 194 0.0 90 2.2 96 0.0 380 0.5
69 CGCTTGTCT g.48620A>G CGGTCAGAG Exon 16 T619A 194 0.0 90 1.1 96 0.0 380 0.3
70 CAGAGCTGC g.48634A>G GATACCATC Exon 16 A623A 194 0.0 90 1.1 96 0.0 380 0.3
43 GAAGATGAC g.49653A>G TGCTTGCGA Exon 17 M677V 190 4.2 86 14.0 88 0.0 364 5.5
71 CCGGCAAC g.53835G>A CTCCAAGTC Exon 18 R698H 196 0.5 82 0.0 94 0.0 372 0.3
72 GAACCTCCA g.53876T>C TAGCTGTTG Exon 18 L712L 196 0.5 82 0.0 94 0.0 372 0.3
44 TTAATATAA g.59981C>A CCTCTCTCT Intron 18 192 43.2 84 21.4 90 27.8 366 34.4
45 AATAGATTT g.73116_73119delATTT TTCTATTTA Intron 19 192 0.0 66 6.1 96 0.0 354 1.1
46 ATTTATAAT g.73132_73133insCAA AAAGTTACT Intron 19 194 0.0 66 6.1 96 0.0 356 1.1
47 ACTTTCTTG g.73148T>C TTACTATCT Intron 19 196 69.4 66 93.9 96 0.0 358 82.1
48 TTTTGTAGC g.73233A>G ATGGGCTGT Exon 20 A804A 200 0.0 66 93.9 96 0.0 362 1.1
49 CTACAGATG g.73505C>T TTCCCAAGT Exon 21 A865V 178 0.0 74 0.0 82 2.4 334 0.6
73 TGGGAGGGG g.73539A>G AATAGAAGT Intron 21 176 0.6 74 0.0 84 0.0 334 0.3
74 TGGTAAAAG g.81650C>T GACTGTGTG Intron 21 196 0.0 86 1.2 94 0.0 376 0.3
75 GTCACGAAA g.82653G>A GAGTTATTT Intron 22 136 0.0 90 0.0 46 2.2 272 0.4
50 GTTATTTCT g.82665G>A CCCTTGTAT Intron 22 202 0.0 92 6.5 82 0.0 376 1.6
76 AGGAGAGGC g.82759G>A GTTCATTGA Exon 23 R958Q 202 0.0 92 0.0 94 1.1 388 0.3
77 CAATATTTA g.82829C>T GGATTCTGC Exon 23 Y981Y 200 0.0 92 1.1 94 0.0 386 0.3
78 GTTTATTGC g.82871G>A AATTCTGCT Exon 23 A995A 200 0.0 92 1.1 94 0.0 386 0.3
51 ACTGAGTGC g.85620A>G ACAGCTCTT Exon 24 A1028A 194 54.1 76 26.3 90 47.8 360 47.8
79 CTATGCAGC g.85774C>A ATAAAAAAG Intron 24 194 0.0 76 0.0 90 1.1 360 0.3
80 GCAAACTAA g.85848C>G ACAAGAACA Intron 24 194 0.0 76 1.3 90 0.0 360 0.3
52 TAAATTTAC g.87308A>G TATCCTTCT Exon 25 T1086T 186 0.0 76 7.9 82 0.0 344 1.7
53 CAATCATGC g.94270A>G TCTTTGCAT Intron 27 172 55.2 64 75.0 94 51.1 330 48.2
81 CCAGAACGC g.94387G>A GATATCATT Exon 28 A1283A 194 0.0 64 0.0 94 1.1 352 0.3
82
TCCCAGCAG
g.94582G>A
AGGGATTGT
Exon 28
192
0.0
26
0.0
88
1.1
306
0.3

  • n, number of alleles analyzed (number of subjects times 2); %, allele frequencies for Caucasians (CA), African Americans (AA), and Japanese (JA).