Variant report

Variant	rs13029217
Chromosome Location	chr2:182063855-182063856
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10171108	0.85[JPT][hapmap]
rs10171998	0.85[JPT][hapmap]
rs10187842	0.85[JPT][hapmap]
rs10211135	0.82[ASN][1000 genomes]
rs10930950	0.85[JPT][hapmap]
rs11678840	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11684463	0.92[ASN][1000 genomes]
rs11692430	0.83[AMR][1000 genomes]
rs11692625	0.88[AMR][1000 genomes]
rs11693055	0.85[AMR][1000 genomes]
rs13002424	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13020845	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs13033038	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13035276	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34366526	0.93[ASN][1000 genomes]
rs34405919	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34467063	0.86[AMR][1000 genomes]
rs34700861	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34774580	0.83[AMR][1000 genomes]
rs34790351	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35110674	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35190308	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35250663	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35357451	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35598315	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35702511	0.88[AMR][1000 genomes]
rs4432412	0.93[ASN][1000 genomes]
rs4514840	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4990275	0.85[JPT][hapmap]
rs56085338	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56096261	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56692685	0.81[AMR][1000 genomes]
rs6433883	0.85[JPT][hapmap]
rs6706397	0.85[JPT][hapmap];0.85[MEX][hapmap]
rs6709702	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6710650	0.85[JPT][hapmap]
rs6713632	0.93[ASN][1000 genomes]
rs6716261	0.85[AMR][1000 genomes]
rs6719732	0.85[AMR][1000 genomes]
rs6724365	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6744130	0.85[JPT][hapmap]
rs6745190	0.85[JPT][hapmap]
rs6752921	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72888919	0.83[AMR][1000 genomes]
rs72890540	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7371639	0.85[JPT][hapmap]
rs7569991	0.85[JPT][hapmap];0.85[MEX][hapmap]
rs7581267	0.86[AMR][1000 genomes]
rs7598010	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9808318	0.82[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	esv1010652	chr2:182062142-182065110	Enhancers Weak transcription Flanking Active TSS Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13029217	ITGA4	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:182056600-182068000	Weak transcription	HSMMtube	muscle
2	chr2:182059800-182064400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:182060000-182064400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr2:182060200-182064800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:182060400-182064000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr2:182061000-182064000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr2:182061000-182064800	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr2:182061000-182065800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr2:182061200-182064400	Enhancers	Primary T cells from cord blood	blood
10	chr2:182061800-182064000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:182061800-182064000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:182063200-182067000	Weak transcription	HSMM	muscle
13	chr2:182063400-182064000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:182063400-182064800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr2:182063400-182068800	Weak transcription	Dnd41	blood
16	chr2:182063600-182064200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:182063600-182065000	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr2:182063600-182065800	Enhancers	Primary T helper cells PMA-I stimulated	--

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