Variant report

Variant	rs10839516
Chromosome Location	chr11:6164628-6164629
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1038006	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10431012	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769667	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769668	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769669	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10839509	0.82[ASN][1000 genomes]
rs10839510	0.82[ASN][1000 genomes]
rs10839512	0.82[ASN][1000 genomes]
rs10839513	0.82[ASN][1000 genomes]
rs10839514	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10839515	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11040741	0.82[ASN][1000 genomes]
rs11040750	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11040760	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11040761	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11040764	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12360715	0.82[ASN][1000 genomes]
rs12787237	0.80[ASN][1000 genomes]
rs12807547	0.82[ASN][1000 genomes]
rs1304843	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1381911	0.82[CEU][hapmap]
rs1462983	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[ASN][1000 genomes]
rs1841821	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1961065	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1964539	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2100884	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2344355	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs2344356	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs325640	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs34481020	0.81[ASN][1000 genomes]
rs34814525	0.81[ASN][1000 genomes]
rs35349232	0.81[ASN][1000 genomes]
rs35682479	0.81[ASN][1000 genomes]
rs4758090	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4758391	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5005636	0.81[ASN][1000 genomes]
rs5005637	0.81[ASN][1000 genomes]
rs5005638	0.81[ASN][1000 genomes]
rs5005639	0.82[ASN][1000 genomes]
rs5005640	0.81[ASN][1000 genomes]
rs5005643	0.82[ASN][1000 genomes]
rs5005644	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv553241	chr11:5506034-6203685	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv530216	chr11:5614439-6468232	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv1036389	chr11:5695451-6177680	Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv540943	chr11:5695451-6177680	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
5	nsv522884	chr11:6144998-6164700	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
6	nsv467697	chr11:6144998-6164700	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
7	nsv553370	chr11:6144998-6164700	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10839516	C16orf82	trans	cerebellum	SCAN
rs10839516	OR52N2	cis	parietal	SCAN
rs10839516	TSPAN32	cis	parietal	SCAN
rs10839516	TMEM9B	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:6160800-6164800	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr11:6163600-6164800	Enhancers	H9 Cell Line	embryonic stem cell
3	chr11:6163800-6165000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:6164000-6165400	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr11:6164400-6164800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
6	chr11:6164400-6164800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr11:6164600-6165400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr11:6164600-6165400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr11:6164600-6165400	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr11:6164600-6165400	Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links