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. 2004 Jul;14(7):1333–1344. doi: 10.1101/gr.1965304

Table 3.

List of Polymorphic Sites Identified by Representing CEPH 1420-02 and 1333-01 in the High LD Interval Surrounding 3435C>T

Namea Location dbSNPIDb Position (bp)c CEPH 142002 CEPH 133301 Target sequence MAF in CEPHse r2 vs 3435C>Tf
1236C>T Exon 12 rs1128503 12413817 CC TT TCTTGAAGGGyCTGAACCTGA 0.47 0.13
IVS 13+24 T>C Intron 13 rs2235033 12413359 CC TT GCCCTTTGCCyTTCTAGAGGT 0.45 0.30
IVS 13+81 C>T Intron 13 rs2235035 12413302 CT CC TAGGAAACTAyTATAAATCGG
IVS 14+38 G>A Intron 14 rs2235013 12412842 AA GG TGATTTATAArCATAAGAACA 0.45 0.31
IVS 14+2201 C>T Intron 14 ss20398881 12410679 CC TT TTGCTAGTTAyTAGAGAGACA 0.44 0.30
IVS 14+3038 G>A Intron 14 ss20398882 12409842 AG GG CACCACGCCCrGCCCAAGCCC
IVS 15+675 G>A Intron 15 rs2091766 12408720 AG GG GGTGGTTTTCrTTTTCAAATA
IVS 16+73 G>A Intron 16 rs2235046 12408282 GG AA CTAGGGCTACrGTAGGAGTGG 0.49 0.37
IVS 17+1786 A>Gd Intron 17 rs4728700 12405875 GG AA TTCTGGAGATrGTTGCCAGGA 0.46 0.42
IVS 17+1918 A>G Intron 17 rs10276603 12405743 AG AA CTCTTCAAAArTCCTTGTTGT
IVS 17+2062 T>C Intron 17 rs4148736 12405599 CT CC GAATGGTTATyCTCTGTGTTC
IVS 17+2293 A>G Intron 17 rs4148737 12405368 AA AG TTTTCCCCAGrCACCTTGGGA
IVS 18+656 G>A Intron 18 ss20398883 12404233 AG GG TTGGGAGGCCrAGGTGAGTGG
IVS 18+971 T>G Intron 18 ss20398884 12403918 TT GT AAGTGCTCCTkGTACCTGTTT
IVS 18+1004 A>G Intron 18 rs10268314 12403885 AG AA CCTTGGGCACrTAAGTAAACT
IVS 18+1317 A>G Intron 18 ss20398885 12403572 AA AG CCTCACTGGGrAATTTGACCT
IVS 20+788 T>C Intron 20 rs10248420 12399202 CT TT AATGAGGAAAyACATAGAGTT
IVS 20+882 A>Td Intron 20 rs10234411 12399108 TT AA AGCTCCTCTTwGTAATTGTTG 0.49 0.42
IVS 20+1545 A>G Intron 20 ss20398887 12398445 AG AA TTTTTTAAAGrGACAGGGTCT
IVS 20+2725 A>G Intron 20 rs4148738 12397265 AA GG TTTGGCTGACrGGTTTTAGTT 0.47 0.41
IVS 20+2758 A>G Intron 20 ss20398888 12397232 AG AA CCTAGTCTTTrCAATGAAAAT
IVS 20+4254 A>G Intron 20 ss20398889 12395736 AG AA GATGTGCTGGrCTAAATTATA
2677G>T,A Exon 21 rs2032582 12394834 GG TT ACTAGAAGGTkCTGGGAAGGT 0.47 0.32
IVS 21+49 T>C Intron 21 rs2032583 12394777 CT TT TAAAGTATTCyAATCAGTGTT
IVS 21+597 C>G Intron 21 ss20398890 12394229 CC CG ATGGAAAAATsCTAGGGGTAT
IVS 21+614 T>A Intron 21 ss20398891 12394212 TT AT GTATTTATTAwATCTGTTTTA
IVS 21+1574 C>A Intron 21 ss20398861 12393252 AC CC AGAAAGCATTmTAGTTAACAG
IVS 21+2425 A>C Intron 21 ss20398862 12392401 AA CC ATTGCCTCTGmTCTTCTCTTG 0.50 0.41
IVS 21+2964 A>T Intron 21 ss20399352 12391862 AA AT ACACAAACCTwTAATTAAAAA
IVS 21+3027 G>Td Intron 21 rs2373586 12391799 GG TT ACCATATAAGkCACCATTCAC 0.47 0.34
IVS 21+5964 T>C Intron 21 ss20398863 12388862 CT TT TAAACTTGTTyATTTGAGGGT
IVS 21+7026 T>G Intron 21 ss20398864 12387800 GT GT AAGTATCTTGkGGTAAACATA
IVS 21+7394 A>G Intron 21 ss20398865 12387432 AG GG AATTCTGGAArTTATTTCTCT
IVS 21+7473 A>G Intron 21 ss20398866 12387353 AG AA CAAATGAGGArAATGAGACAG
IVS 21+7724 G>A Intron 21 ss20398867 12387102 AG GG ACGCCATCTTrACTCACTGCA
IVS 21+7987 A>T Intron 21 ss20398868 12386839 AT AA TATGTGCCACwTTCCTTAAAA
IVS 21+8099 C>T Intron 21 ss20398869 12386727 CT CC GTGTGTGAGGyTGCAGTGAGC
IVS 21+8507 T>C Intron 21 rs4148740 12386319 TT CT AAAAAAACAAyATGGAAATGT
IVS 21+8565 T>C Intron 21 rs4148742 12386261 CT TT TATTCAGCATyATGATCAGAC
IVS 21+8952 G>A Intron 21 rs2373589 12385874 AG GG TCATGGTTTGrCAAAGTACTG
IVS 21+9086 C>G Intron 21 rs1882477 12385740 CG GG TTGCTTCCATsATTACCAAAT
IVS 21+9520 G>A Intron 21 rs4148743 12385306 AA GG TATCTTTTTCrCAGTTGGGTG 0.45 0.19
IVS 23+314 G>A Intron 23 ss20398870 12382544 GG AG CCTGAGCAAGrAGTCTGACTG
IVS 25+1986_1991_del Intron 25 ss20398871 12376777 +/+ -/- AGCCTCC[[TTTTC]/-]TTTCACT 0.48 0.48
IVS 25+2733 G>A Intron 25 ss20398872 12376030 GG AA TTGACCTGAArTGGTGGTTCT 0.49 0.50
IVS 25+3050 G>T Intron 25 ss20398873 12375713 GG TT (A)12(T)9kAATGCAAAAT 0.40 0.73
IVS 25+3739 T>C Intron 25 ss20398874 12375024 CT TT AATTATTATTyCACAGTAAAT 0.19 0.25
IVS 25+4091 C>T Intron 25 ss20398875 12374672 CT CT GTTTGCAATTyTAGGGTATTA
IVS 25+4983 T>G Intron 25 ss20398876 12373780 GT GT TCCATGCTAAkCCTGGGCACT
IVS 25+5231 T>C Intron 25 ss20398880 12373532 CC TT TGATCTGTTTyCTTGCTTGTG 0.42 0.79
3435C>T Exon 26 rs1045642 12372861 CC TT AGGAAGAGATyGTGAGGGCAG 0.42 1.00
IVS 26+80 T>C Intron 26 rs2235048 12372727 TT CC AGGGGCTGGTyTCCCAGAAGT 0.43 0.91
IVS 26+1113 C>T Intron 26 ss20398877 12371694 CT CC TATTAAAAGTyCAAAATTAGA 0.05 0.03
IVS 26+1130 C>T Intron 26 ss20398878 12371677 CT CC TAGATTTTTTyCAACCTTTAT 0.23 0.35
IVS 26+1573 A>G Intron 26 rs1882478 12371234 AG GG TCAACCCGGCrGGGAAGACAG 0.25 0.36
IVS 26+1576 G>A Intron 26 ss20398879 12371231 AG GG ACCCGGCGGGrAAGACAGTTT 0.22 0.31
a

For exonic SNPs, the locus name refers to the base position in the ABCB1 cDNA (GenBank acc. no. M14758), with the first base of the ATG start set to 1. Intronic SNPs were named as follows: the intron number was followed by a number indicating the distance from the G of the donor site invariant GT immediately upstream of the SNP. bSNP position within the reference contig (GenBank acc. no. NT_007933). The ancestral state of the polymorphism was determined either by sequencing a chimpanzee sample, or assuming that the ancestral state was the most frequent allele in our sample. For SNPs marked with dthis information is missing. cThe new variants were deposited in the GenBank database (ss ID above). eMAF (minor allele frequency), and fr2 (posterior mean) against 3435C>T were calculated in unrelated CEPH chromosomes only for the newly identified homozygous sites, and for the heterozygous sites located in the region downstream IVS 25+3050 G>T.