Table 1. Polymorphisms of the VCAM1... | American Society of Hematology

Table 1.

Polymorphisms of the VCAM1 locus identified by sequence analysis

VCAM1 region	Nucleotide position^8-150	Amino acid position	SNP typology classification^8-151	Variant alleles observed^8-152	dbSNP identifier^8-153
5′ upstream	A−2062C	—	VI	1	rs3783595
	C−2021T	—	VI	37	rs1409419
	C−1698G	—	VI	3	rs3783597
	T−1599G	—	VI	8	rs3783598
	T−1592C	—	VI	8	rs1041163
	T−1530C	—	VI	3	rs3783599
	T−1379C	—	VI	1	rs3783600
	A−1356G	—	VI	3	rs3783601
	A−1242T	—	VI	2	rs3181087
	G−1148A	—	VI	3	rs3783603
	T−833C	—	VI	10	rs3170794
	A−540G	—	VI	1	rs3783605
	T−383G	—	VI	1	rs3783606
cDNA
5′ UTR	C−118T	—	IV	1	rs3783607
5′ UTR	C−109T	—	IV	8	rs3783608
5′ UTR	G−54A	—	IV	8	rs3783609
5′ UTR	G−14C	—	IV	1	rs3783610
Ig domain 4	C953T	S318F	I	3	rs3783611
Ig domain 4	A1150G	T384K	I	3	rs3783612
Ig domain 5	G1238C	G413A	II	5	rs3783613
TMD	C2079T	D693D	III	15	rs3176878
TMD	A2146T	I716L	II	4	rs3783615
TMD	A2208G	K736K	III	19	rs3176879
3′ UTR	G2262C	—	V	1	rs3783617
3′ UTR	C2507A	—	V	2	rs3783618
3′ UTR	A2548G	—	V	1	rs3783619
3′ UTR	G2844A	—	V	1	rs3783620
3′ UTR	C2876A	—	V	2	rs3783621
Other noncoding
Intron 3^8-150	C4757T	—	VI	3	rs2392221
Intron 7^8-150	A14563G	—	VI	5	rs3176875
3′ downstream^8-150	A19228G	—	VI	20	rs3181092
3′ downstream^8-150	C19312T	—	VI	6	rs3181093
3′ downstream^8-150	A19382G	—	VI	3	rs3783624

VCAM1 region	Nucleotide position^8-150	Amino acid position	SNP typology classification^8-151	Variant alleles observed^8-152	dbSNP identifier^8-153
5′ upstream	A−2062C	—	VI	1	rs3783595
	C−2021T	—	VI	37	rs1409419
	C−1698G	—	VI	3	rs3783597
	T−1599G	—	VI	8	rs3783598
	T−1592C	—	VI	8	rs1041163
	T−1530C	—	VI	3	rs3783599
	T−1379C	—	VI	1	rs3783600
	A−1356G	—	VI	3	rs3783601
	A−1242T	—	VI	2	rs3181087
	G−1148A	—	VI	3	rs3783603
	T−833C	—	VI	10	rs3170794
	A−540G	—	VI	1	rs3783605
	T−383G	—	VI	1	rs3783606
cDNA
5′ UTR	C−118T	—	IV	1	rs3783607
5′ UTR	C−109T	—	IV	8	rs3783608
5′ UTR	G−54A	—	IV	8	rs3783609
5′ UTR	G−14C	—	IV	1	rs3783610
Ig domain 4	C953T	S318F	I	3	rs3783611
Ig domain 4	A1150G	T384K	I	3	rs3783612
Ig domain 5	G1238C	G413A	II	5	rs3783613
TMD	C2079T	D693D	III	15	rs3176878
TMD	A2146T	I716L	II	4	rs3783615
TMD	A2208G	K736K	III	19	rs3176879
3′ UTR	G2262C	—	V	1	rs3783617
3′ UTR	C2507A	—	V	2	rs3783618
3′ UTR	A2548G	—	V	1	rs3783619
3′ UTR	G2844A	—	V	1	rs3783620
3′ UTR	C2876A	—	V	2	rs3783621
Other noncoding
Intron 3^8-150	C4757T	—	VI	3	rs2392221
Intron 7^8-150	A14563G	—	VI	5	rs3176875
3′ downstream^8-150	A19228G	—	VI	20	rs3181092
3′ downstream^8-150	C19312T	—	VI	6	rs3181093
3′ downstream^8-150	A19382G	—	VI	3	rs3783624

We amplified 5962 base pairs of the VCAM1coding sequence (GenBank accession number XM_035776) or flanking regions as 19 different PCR products in 40 healthy African Americans. PCR products were sequenced in both directions to identify common genetic variants. A total of 33 biallelic single nucleotide polymorphisms (SNPs) were detected.

Ig indicates immunoglobulin; TMD, transmembrane domain; and —, noncoding sequence.

F8-150

Nucleotide positions for the cDNA SNPs are relative to the ATG of the coding (translated) region. Positions for the 5′ upstream and “Other noncoding” SNPs are relative to the ATG on genomic contig NT_004308. Alternatively, the nucleotide positions of the “Other noncoding” SNPs refer to position 1277 of intron 3 (Int3 + 1277), position 1739 of intron 7 (Int7 + 1739), and positions + 46, + 130, and + 200 downstream from the 3′ end of cDNA XM_035776.

F8-151

SNP Typology Classification as proposed by Risch8 where Class I equals nonsynonymous coding with nonconservative amino acid change; Class II equals nonsynonymous coding with conservative amino acid change; Class III equals synonymous coding (no amino acid change); Class IV equals 5′ untranslated region (5′ UTR of cDNA); Class V equals 3′ UTR; and Class VI equals other noncoding regions (including introns, promoters, and intergenic regions).

F8-152

The number of variant alleles observed in a population of 80 chromosomes is indicated.

F8-153

National Center for Biotechnology Information Database of Single Nucleotide Polymorphisms (http://www.ncbi.nlm.nih.gov/SNP/).

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