Variant report

Variant	rs4514840
Chromosome Location	chr2:182045274-182045275
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10171108	1.00[JPT][hapmap]
rs10171998	1.00[JPT][hapmap]
rs10187842	1.00[JPT][hapmap]
rs10930950	1.00[JPT][hapmap]
rs11678840	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11684463	0.83[ASN][1000 genomes]
rs11688120	0.81[AMR][1000 genomes]
rs11692430	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11692625	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11693055	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12989967	1.00[JPT][hapmap]
rs13002424	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13020845	0.85[JPT][hapmap];0.86[MEX][hapmap]
rs13029217	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13029368	1.00[JPT][hapmap]
rs13033038	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13035276	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34366526	0.84[ASN][1000 genomes]
rs34405919	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34467063	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34700861	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34774580	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34790351	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34825850	0.83[AMR][1000 genomes]
rs35076700	0.83[AMR][1000 genomes]
rs35110674	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35190308	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35250663	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35357451	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35598315	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35702511	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35725888	0.83[AMR][1000 genomes]
rs4346343	0.86[JPT][hapmap]
rs4366861	0.86[JPT][hapmap]
rs4432412	0.84[ASN][1000 genomes]
rs4667008	0.86[JPT][hapmap]
rs4990275	1.00[JPT][hapmap]
rs56085338	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56096261	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56692685	0.85[AMR][1000 genomes]
rs6433883	1.00[JPT][hapmap]
rs6433892	0.86[JPT][hapmap]
rs6706397	0.86[MEX][hapmap]
rs6709702	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6710650	1.00[JPT][hapmap]
rs6713632	0.84[ASN][1000 genomes]
rs6716261	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6719732	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6724365	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6731268	1.00[JPT][hapmap]
rs6744130	1.00[JPT][hapmap]
rs6745190	1.00[JPT][hapmap]
rs6752921	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72887083	0.83[AMR][1000 genomes]
rs72888919	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72890540	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7371639	1.00[JPT][hapmap]
rs7559803	1.00[JPT][hapmap]
rs7569991	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs7581267	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7598010	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9808318	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431824	chr2:181946115-182118559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv961739	chr2:182041759-182049669	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4514840	ITGA4	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182031800-182050400	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr2:182032400-182048400	Weak transcription	Fetal Thymus	thymus
3	chr2:182035200-182048800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:182043800-182048400	Weak transcription	GM12878-XiMat	blood
5	chr2:182043800-182053200	Weak transcription	Primary T cells from cord blood	blood
6	chr2:182044000-182054400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr2:182044000-182055400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:182044600-182048800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:182044800-182045400	ZNF genes & repeats	Dnd41	blood
10	chr2:182045000-182045400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:182045000-182050600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr2:182045000-182053400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:182045000-182053600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr2:182045200-182047800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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