Variant report

Variant	rs6984496
Chromosome Location	chr8:10796093-10796094
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10096381	0.81[CEU][hapmap]
rs10107145	0.96[CEU][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs11250092	0.96[CEU][hapmap];1.00[CHD][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11250093	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11250094	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11250099	0.81[CEU][hapmap];0.80[TSI][hapmap]
rs11776368	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11777007	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11783247	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap]
rs11783749	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11986699	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11990550	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11993591	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12542037	0.92[CEU][hapmap]
rs12546366	0.91[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap]
rs2409692	1.00[CHB][hapmap]
rs34741518	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4073948	0.81[EUR][1000 genomes]
rs4240671	0.81[CEU][hapmap];0.89[TSI][hapmap]
rs4240673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap]
rs4326350	0.81[GIH][hapmap];0.87[TSI][hapmap]
rs4520127	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4841457	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4841458	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4841460	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4841461	0.83[ASN][1000 genomes]
rs4841465	0.85[CEU][hapmap]
rs6601544	0.81[CEU][hapmap]
rs6985109	0.96[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs6988281	1.00[CHB][hapmap]
rs6992103	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6996943	0.83[CEU][hapmap]
rs7005884	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7015168	1.00[CHB][hapmap]
rs7016385	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7814762	0.83[ASN][1000 genomes]
rs7823296	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7833435	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7837038	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7843470	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917085	chr8:10237508-10828204	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1017836	chr8:10591801-10803617	Enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1034988	chr8:10591801-10804243	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1025190	chr8:10756331-10802566	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6984496	C8orf5	Cis_1M	lymphoblastoid	RTeQTL
rs6984496	BLK	Cis_1M	lymphoblastoid	RTeQTL
rs6984496	C8orf13	cis	multi-tissue	Pritchard
rs6984496	AF131215.2	cis	Nerve Tibial	GTEx
rs6984496	CLDN23	cis	multi-tissue	Pritchard

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10795400-10796200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:10795400-10796200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr8:10795400-10796400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr8:10795600-10796200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr8:10795600-10796200	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr8:10795600-10796200	Active TSS	Brain Anterior Caudate	brain
7	chr8:10795800-10805800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr8:10796000-10796200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr8:10796000-10796200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr8:10796000-10796200	Flanking Active TSS	H9 Cell Line	embryonic stem cell
11	chr8:10796000-10799800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links