Variant report

Variant	rs13031518
Chromosome Location	chr2:181991759-181991760
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10171108	0.85[JPT][hapmap]
rs10171998	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10187842	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10930950	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs11688120	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11692430	0.81[EUR][1000 genomes]
rs11692625	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11693055	0.85[EUR][1000 genomes]
rs11893772	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11893821	0.94[ASN][1000 genomes]
rs12621277	0.82[JPT][hapmap]
rs12999974	0.94[ASN][1000 genomes]
rs13004683	0.85[ASN][1000 genomes]
rs13004750	0.87[ASN][1000 genomes]
rs13011738	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13011751	0.88[EUR][1000 genomes]
rs13012524	0.88[EUR][1000 genomes]
rs13020845	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs13026070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13029368	0.85[JPT][hapmap]
rs13033038	0.81[AFR][1000 genomes]
rs13033467	0.94[ASN][1000 genomes]
rs34467063	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34504038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34714467	0.94[ASN][1000 genomes]
rs34774580	0.85[EUR][1000 genomes]
rs34825850	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35076700	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35323141	0.98[ASN][1000 genomes]
rs35482602	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35543145	0.94[ASN][1000 genomes]
rs35702511	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35725888	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4346343	0.82[CHB][hapmap]
rs4366861	0.82[CHB][hapmap];0.86[MEX][hapmap]
rs4510177	0.82[CHB][hapmap]
rs4595925	0.82[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs4667005	0.86[MEX][hapmap]
rs4990275	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs55900432	0.94[ASN][1000 genomes]
rs55954384	0.94[ASN][1000 genomes]
rs56692685	0.85[EUR][1000 genomes]
rs59639779	0.94[ASN][1000 genomes]
rs6433878	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6433879	0.82[CHB][hapmap]
rs6433883	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6433892	0.82[CHB][hapmap]
rs6704750	0.82[CHB][hapmap]
rs6706397	0.85[JPT][hapmap];1.00[MEX][hapmap]
rs6710650	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6716261	0.85[EUR][1000 genomes]
rs6719732	0.85[EUR][1000 genomes]
rs6743720	0.84[ASN][1000 genomes]
rs6744130	0.82[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs6745190	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6746347	0.94[ASN][1000 genomes]
rs6759865	0.94[ASN][1000 genomes]
rs72887083	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72888919	0.85[EUR][1000 genomes]
rs7349232	0.87[ASN][1000 genomes]
rs7371639	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7558428	0.94[ASN][1000 genomes]
rs7559803	0.85[JPT][hapmap];0.86[MEX][hapmap]
rs7569991	0.82[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap]
rs7581267	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7598960	0.94[ASN][1000 genomes]
rs9808318	0.82[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv459954	chr2:181975252-182040293	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv583910	chr2:181975252-182040293	ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13031518	ITGA4	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:181989000-181992000	Weak transcription	NHEK	skin
2	chr2:181990600-181994200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr2:181990600-181995600	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr2:181990800-181992800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr2:181991000-181991800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
6	chr2:181991200-181992400	Weak transcription	GM12878-XiMat	blood
7	chr2:181991400-181991800	Enhancers	Fetal Thymus	thymus
8	chr2:181991400-181992200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:181991400-181992800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr2:181991400-181993000	Enhancers	Dnd41	blood
11	chr2:181991400-181996000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:181991400-181996200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:181991600-181992000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr2:181991600-181992400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr2:181991600-181992600	Enhancers	Primary T cells from cord blood	blood
16	chr2:181991600-181992600	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:181991600-181992600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr2:181991600-181992600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:181991600-181992800	Enhancers	Primary T killer memory cells from peripheral blood	blood

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