Variant report

Variant	rs990716
Chromosome Location	chr5:35899264-35899265
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr5:35898840-35899745	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr5:35898998-35899530	H1-neurons	neurons:	n/a	n/a
3	CCNT2	chr5:35899202-35899353	K562	blood:	n/a	n/a
4	POLR2A	chr5:35899111-35899476	H1-neurons	neurons:	n/a	n/a
5	REST	chr5:35899023-35899627	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:35849089..35851096-chr5:35897625..35900411,2	K562	blood:

Variant related genes	Relation type
ENSG00000248349	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1008756	1.00[ASN][1000 genomes]
rs1010599	1.00[ASN][1000 genomes]
rs1010601	1.00[ASN][1000 genomes]
rs1025039	1.00[ASN][1000 genomes]
rs10491434	0.88[CEU][hapmap];0.84[GIH][hapmap];0.85[EUR][1000 genomes]
rs10491435	0.85[EUR][1000 genomes]
rs1053496	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs11567685	0.84[EUR][1000 genomes]
rs11567699	0.88[CEU][hapmap];0.84[GIH][hapmap];0.84[EUR][1000 genomes]
rs11567701	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs11567751	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs11949691	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950831	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11960511	0.88[EUR][1000 genomes]
rs1345827	1.00[ASN][1000 genomes]
rs1494554	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1494571	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs16902573	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17376481	1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[LWK][hapmap];0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs1833907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2194224	0.91[ASN][1000 genomes]
rs2287900	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2361403	0.91[ASN][1000 genomes]
rs3194051	0.88[CEU][hapmap];0.84[GIH][hapmap];0.86[EUR][1000 genomes]
rs3822733	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs3866449	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4024109	0.83[ASN][1000 genomes]
rs4024110	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55654952	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57545288	0.80[EUR][1000 genomes]
rs59030624	1.00[ASN][1000 genomes]
rs62351973	0.90[EUR][1000 genomes]
rs62355272	0.81[EUR][1000 genomes]
rs67207043	0.88[EUR][1000 genomes]
rs6859465	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6862692	1.00[ASN][1000 genomes]
rs6871116	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6873195	0.81[ASN][1000 genomes]
rs6878577	0.94[ASN][1000 genomes]
rs6878688	1.00[ASN][1000 genomes]
rs700179	0.85[EUR][1000 genomes]
rs72742471	0.94[ASN][1000 genomes]
rs7702587	0.84[ASN][1000 genomes]
rs7702828	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7705615	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719334	0.94[ASN][1000 genomes]
rs7723452	0.91[ASN][1000 genomes]
rs9764914	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9765078	0.94[ASN][1000 genomes]
rs984164	1.00[ASN][1000 genomes]
rs987107	0.88[CEU][hapmap];0.84[GIH][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022761	chr5:35775802-35902546	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv471011	chr5:35861068-36003217	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv830261	chr5:35863084-36018048	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35891400-35902400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:35893600-35899400	Enhancers	Dnd41	blood
3	chr5:35897600-35899600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr5:35898800-35899600	Enhancers	Thymus	Thymus
5	chr5:35898800-35899800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:35899000-35899800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr5:35899000-35900200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:35899000-35901400	Enhancers	GM12878-XiMat	blood
9	chr5:35899000-35902800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr5:35899000-35903000	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr5:35899000-35903400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:35899000-35906000	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr5:35899000-35909200	Enhancers	Fetal Thymus	thymus
14	chr5:35899200-35899400	Enhancers	Pancreatic Islets	Pancreatic Islet
15	chr5:35899200-35899800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr5:35899200-35899800	Enhancers	NHDF-Ad	bronchial
17	chr5:35899200-35903000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr5:35899200-35903400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:35899200-35905400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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