Variant report

Variant	rs6451231
Chromosome Location	chr5:35878927-35878928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10044838	1.00[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10044883	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10058453	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10063445	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10074095	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10074127	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10941267	1.00[CEU][hapmap];0.96[GIH][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11567686	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11567737	1.00[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11567762	0.82[JPT][hapmap]
rs1353250	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1353252	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1389830	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1389831	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1389832	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1494555	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1494556	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1494557	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1494558	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1494560	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1494561	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1494562	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1862634	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3777090	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6451226	1.00[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6451227	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6451228	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6451230	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6893142	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7701111	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7711202	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7711208	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7711268	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7716064	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7720993	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9292616	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292617	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs969129	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6451231	NIPBL	cis	parietal	SCAN
rs6451231	WDR70	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35860400-35883800	Weak transcription	Small Intestine	intestine
2	chr5:35866600-35882000	Genic enhancers	Dnd41	blood
3	chr5:35867800-35879800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr5:35873200-35880200	Genic enhancers	Primary T cells from cord blood	blood
5	chr5:35873200-35880200	Genic enhancers	Thymus	Thymus
6	chr5:35873400-35880000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr5:35875400-35883200	Genic enhancers	Fetal Thymus	thymus
8	chr5:35876600-35884600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:35876800-35883600	Weak transcription	Osteobl	bone
10	chr5:35877000-35879200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr5:35877000-35879200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:35877000-35879200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:35877000-35880400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr5:35877200-35879200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr5:35877400-35879800	Strong transcription	NHLF	lung
16	chr5:35877400-35883600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:35877600-35883200	Weak transcription	NHEK	skin
18	chr5:35877800-35881000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:35878000-35879200	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr5:35878000-35881000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr5:35878000-35882000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:35878000-35882000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:35878000-35882200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr5:35878200-35879000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr5:35878200-35879800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
26	chr5:35878200-35880000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:35878200-35883600	Weak transcription	HSMM	muscle
28	chr5:35878400-35879000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr5:35878400-35880400	Weak transcription	Hela-S3	cervix
30	chr5:35878400-35882600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr5:35878800-35879000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr5:35878800-35880000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr5:35878800-35880400	Enhancers	Primary T helper naive cells from peripheral blood	blood

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