Variant report

Variant	rs6881706
Chromosome Location	chr5:35879156-35879157
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10063294	0.94[JPT][hapmap]
rs10213865	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10214237	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10214273	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10472984	0.85[AMR][1000 genomes]
rs11567694	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11567705	0.87[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11742240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742270	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12658443	0.91[ASN][1000 genomes]
rs13188960	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1494564	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34463936	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4594881	0.85[AMR][1000 genomes]
rs62351974	0.81[EUR][1000 genomes]
rs62351975	0.81[EUR][1000 genomes]
rs6871748	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6881270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][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];1.00[ASN][1000 genomes]
rs6890853	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6897932	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7717955	0.84[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs860413	0.83[MEX][hapmap]
rs987106	0.94[JPT][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6881706	DNAJC21	cis	cerebellum	SCAN
rs6881706	C5orf33	cis	cerebellum	SCAN
rs6881706	TOMM7	cis	cerebellum	SCAN
rs6881706	LMBRD2	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	chr5:35878200-35879800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr5:35878200-35880000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr5:35878200-35883600	Weak transcription	HSMM	muscle
27	chr5:35878400-35880400	Weak transcription	Hela-S3	cervix
28	chr5:35878400-35882600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:35878800-35880000	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr5:35878800-35880400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr5:35879000-35879800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:35879000-35880600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr5:35879000-35881800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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