Variant report

Variant	rs6724365
Chromosome Location	chr2:182040293-182040294
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11678840	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11692430	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11692625	0.85[AMR][1000 genomes]
rs11693055	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13002424	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13029217	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13033038	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13035276	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34405919	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34467063	0.83[AMR][1000 genomes]
rs34700861	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34774580	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34790351	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35110674	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35190308	0.88[EUR][1000 genomes]
rs35250663	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35357451	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35598315	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35702511	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4514840	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56085338	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56096261	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56692685	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6709702	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6716261	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6719732	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6752921	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72888919	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72890540	0.85[EUR][1000 genomes]
rs7581267	0.83[AMR][1000 genomes]
rs7598010	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]

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
rs6724365	ITGA4	cis	parietal	SCAN

Chromatin state (count:23 , 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	chr2:182035200-182042800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr2:182035200-182044800	Weak transcription	Dnd41	blood
5	chr2:182035200-182048800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr2:182036200-182041400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:182036400-182042600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr2:182038400-182043200	Enhancers	HSMMtube	muscle
9	chr2:182039200-182040600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:182039400-182040400	Enhancers	GM12878-XiMat	blood
11	chr2:182039600-182040400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr2:182039600-182040400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr2:182039600-182040400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr2:182039600-182040400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr2:182039600-182040400	Enhancers	HSMM	muscle
16	chr2:182039600-182044000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr2:182039800-182040800	Weak transcription	Fetal Brain Male	brain
18	chr2:182040000-182040400	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:182040000-182040400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr2:182040000-182040400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr2:182040200-182040400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr2:182040200-182041200	Weak transcription	Primary T cells from cord blood	blood
23	chr2:182040200-182041200	Weak transcription	NHEK	skin

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