TABLE 2

Allele frequencies of SNPs (in/dels) identified in PXR's promoter and intron 1

Position in AF364606
Position from Translation Start Site (+1)a
Position from Transcription Start Site (+1)b
rs Number (HAPMAP)
PDR (n = 24)
Whites (n = 46)
Region
Effects
Allele1
Allele2
Allele1
Allele2
37345G>A –33045 –8491 G = 0.99 A = 0.01 Upstream
37479T>C –32911 –8357 T = 0.9 C = 0.1 Upstream
38851G>A –31539 –6985 G = 0.98 A = 0.02 Upstream
38982G>A –31408 –6854 rs4688036 A = 0.92 G = 0.08 Upstream
39057G>A –31333 –6779 G = 0.96 A = 0.04 Upstream
39117A>G –31273 –6719 rs9832958 A = 0.78 G = 0.22 Upstream
44477T>C –25913 –1359 rs1523130 (Celera C = 0.67, T = 0.33) C = 0.542 T = 0.45 C = 0.73 T = 0.27 5′UTR STAT1,3,6, NFAT sites lost in T allelec
44578A>G –25812 –1258 G = 0.94 A = 0.06 5′UTR
44664C>A –25726 –1172 C = 0.98 A = 0.02 5′UTR
45005C>T –25385 –831 rs3814055de (PAAR, C = 0.70, T = 0.30) C = 0.71 T = 0.29 C = 0.69 T = 0.31 5′UTR SNP present in NF-κB, ISGF-3 sitesc
45354G>C –25036 –482 G = 0.98 C = 0.02 5′UTR
45387C>T –25003 –449 C = 0.98 T = 0.02 5′UTR (Ex1a)
45634G>A –24756 –202 rs1523128e (PAAR, T = 0.95, C = 0.05) G = 0.92 A = 0.08 5′UTR (Ex1a) C/EBP sites gained in A allele
46370 6bp del –24020 rs3842689 n = 0.71 D = 0.29 5′UTR (Ex1b) HNF1 site lost with deletionc
46555 C ins –23839 rs11421631 5C = 0.71 6C = 0.29 5′UTR (Ex1b) C insertion present in STRE sitec
50041A>T –20349 rs4234666d (G = 0.80, C = 0.20) A = 0.91 T = 0.09 intron1b
50288G>C –20102 G = 0.77 C = 0.23 intron1b
50646C>T –19744 rs4472074 C = 0.92 T = 0.08 intron1b
50666A>G –19724 A = 0.77 G = 0.23 intron1b
50675insC –19715 rs11409387 I = 0.77 n = 0.23 intron1b
51272A>G –19118 A = 0.98 G = 0.02 intron1b
51347C>A –19043 C = 0.98 A = 0.02 intron1b
51555del –18835 rs3030845 D = 0.74 n = 0.26 intron1b
51890G>T –18500 G = 0.95 T = 0.05 intron1b
51945(TTAins) –18445 (TTA)4 = 0.90 (TTA)5 = 0.10 intron1b
51957C>A –18433 C = 0.98 A = 0.02 intron1b Repeat is present in FOXJ2 site
51958G>A –18432 G = 0.98 A = 0.02 intron1b
52056C>A –18334 C = 0.98 A = 0.02 intron1b
52480C>T –17910 C = 0.98 T = 0.02 intron1b
52501C>T –17889 rs4566573 C = 0.98 T = 0.02 intron1b SNP present in DR4 site
52605T>C –17785 T = 0.97 C = 0.03 intron1b
55416A>G –14974 A = 0.90 G = 0.10 A = 0.01 G = 0.99 intron1b
55508C>T –14882 C = 0.99 T = 0.01 intron1b
55835T>C –14555 T = 0.99 C = 0.01 intron1b PPARγ site gained in C allele
55911T>A –14479 T = 0.98 A = 0.02 intron1b
55952G>C –14438 G = 0.96 C = 0.04 G = 0.98 C = 0.02 intron1b SNP present in DR4 site
56130C>G –14260 C = 0.99 G = 0.01 intron1b
56225G>C –14165 G = 0.98 C = 0.02 G = 1.0 C = 0.0 intron1b
56310T>G –14080 T = 0.99 G = 0.01 intron1b
56348C>A –14042 C = 0.56 A = 0.44 C = 0.71 A = 0.29 intron1b SNP present in DR3 sitec
56939A>G –13451 A = 0.98 G = 0.02 intron1b
57001C>T –13389 C = 0.98 T = 0.02 intron1b
57036C>G –13354 C = 0.92 G = 0.08 intron1b
57347C>T –13043 C = 0.96 T = 0.04 intron1b
57552G>A –12838 G = 0.92 A = 0.08 G = 0.98 A = 0.02 intron1b
57610C>G –12780 C = 0.98 G = 0.02 intron1b
57725T>C –12665 T = 0.98 C = 0.02 intron1b
57805A>G –12585 rs6773295 A = 0.90 G = 0.10 A = 0.98 G = 0.02 intron1b
57825G>T –12565 rs6438545 G = 0.90 T = 0.10 G = 0.98 T = 0.02 intron1b
57836A>T –12554 A = 0.98 T = 0.02 intron1b
58105T>G –12285 T = 0.99 G = 0.01 intron1b
58188T>C –12202 rs13085558 T = 0.90 C = 0.10 T = 0.91 C = 0.09 intron1b c
58234G>A –12156 G = 0.96 A = 0.04 intron1b
58638G>A –11752 G = 0.92 A = 0.08 G = 0.97 A = 0.03 intron1b
58850A>T –11540 A = 0.94 T = 0.06 intron1b HNF4 site lost in T allele
58947G>A –11443 G = 0.98 A = 0.02 G = 0.99 A = 0.01 intron1b
58977C>T –11413 C = 0.72 T = 0.28 intron1b
59009G>T –11381 G = 0.64 T = 0.36 intron1b
60877T>C –9513 T = 0.79 C = 0.21 T = 0.97 C = 0.03 intron1b HEB site gained in C allele
62445G>A –7945 G = 0.91 A = 0.09 G = 0.98 A = 0.02 intron1b SNP present in HNF4α and NF1 sites
62449A>G –7941 A = 0.91 G = 0.09 A = 0.98 G = 0.02 intron1b SNP present in NF1 site
62452A>T –7938 A = 0.91 T = 0.09 A = 0.98 T = 0.02 intron1b SNP present in NF1 site
62460C>A –7930 C = 0.91 A = 0.09 C = 0.98 A = 0.02 intron1b
62466A>G –7924 A = 0.83 G = 0.17 A = 0.96 G = 0.04 intron1b
62467A>G –7923 A = 0.91 G = 0.09 A = 0.098 G = 0.02 intron1b
63396C>T –6994 rs2472677 C = 0.75 T = 0.35 C = 0.38 T = 0.62 intron1b SNP present in HNF3β sitec
63448C>A –6942 A = 0.99 C = 0.01 intron1b
63563T>G –6827 T = 0.94 G = 0.06 intron1b
63704A>G –6686 rs12492296 G = 0.75 A = 0.35 G = 0.38 A = 0.62 intron1b c
63813(CAAA)5/6, (CA)12/14 –6577 rs4267673, rs7372335 5/12 = 0.58 6/13 = 0.42 5/12 = 0.62 6/12 = 0.38 intron1b HNF3β site gained by (CAAA)CA insertionc
63877T>C –6513 rs6438546d (T = 0.62, C = 0.38) C = 0.64 T = 0.36 T = 0.63 C = 0.37 intron1b c
66034T>C –4356 rs13059232d (T = 0.43, C = 0.56) T = 0.56 C = 0.44 T = 0.35 C = 0.65 intron1b c
66261G>A –4129 G = 0.96 A = 0.041 intron1b
68162G>T –2228 rs2416818 (G = 0.86, A = 0.14) G = 0.88 T = 0.12 intron1b
68381G>T –2009 rs4688040 G = 0.54 T = 0.46 G = 0.79 T = 0.21 intron1b SNP present in HNF3α sitec
68456G>T –1934 G = 0.80 T = 0.20 intron1b c
68535G>A –1855 T = 0.60 G = 0.40 intron1b
68593T>G –1797 T = 0.98 G = 0.02 intron1b
68618T>C –1772 T = 0.98 C = 0.02 intron1b DR4 site lost in C allele
68707G>A –1683 rs4688041 G = 0.92 A = 0.08 intron1b
68740T>A –1650 rs2472679 T = 0.92 A = 0.08 T = 0.96 A = 0.04 intron1b c
68804C>T –1586 C = 0.98 T = 0.02 intron1b
68895C>A –1495 C = 0.98 A = 0.02 intron1b
68943C>A –1447 rs2461817 A = 0.65 C = 0.35 C = 0.75 A = 0.25 intron1b SNP present in DR3 and C/EBPγ sites
69245C>T –1145 C = 0.95 T = 0.05 intron1b CREB site lost in T allelec
69413G>A –977 G = 0.098 A = 0.02 intron1b
69488A>G –902 A = 0.094 G = 0.04 A = 0.95 G = 0.05 intron1b
69764G>T –626 G = 0.87 T = 0.13 G = 0.98 T = 0.02 intron1b
69789A>G
–601
rs7643645d (G = 0.31, A = 0.69)
G = 0.45
A = 0.55
A = 0.64
G = 0.36
intron1b
HNF4 site lost in G allelec

  • I, insertion; N, normal (WT allele); D, deletion.

    Boxed SNP between 55835 and 56348 are located in the retrotransposed prohibitin pseudogene

  • ↵ a Position in AF364606, +1 being translation start site

  • ↵ b Position relative to transcription start site based on AF061056, +1 being transcription start site

  • ↵ c Italicized SNP showed significant association to traits in study

  • ↵ d Indicates SNP identified in HAPMAP; frequencies are in parentheses

  • ↵ e Indicates SNP identified by Zhang et al. (2001)