Variant report

Variant	rs1460592
Chromosome Location	chr8:112977188-112977189
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:112976579..112977386-chr8:113471922..113472710,2	MCF-7	breast:
2	chr8:112976391..112977811-chr8:113408288..113409205,6	MCF-7	breast:
3	chr8:112976314..112977253-chr8:113408305..113409151,3	MCF-7	breast:
4	chr8:112976625..112977471-chr8:114449676..114450374,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10088291	0.86[EUR][1000 genomes]
rs10505166	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955608	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11775565	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11781758	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11787144	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17812276	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs186489	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2353259	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs320505	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs320507	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs320509	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs320510	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs320512	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs320513	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs320514	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs320515	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs320521	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs320535	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs320541	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs320555	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs396807	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4391464	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs440036	0.89[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap]
rs446737	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4501608	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4876276	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56003701	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56310640	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62520458	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62521976	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62521981	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6469400	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs652101	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs688273	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72670543	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7827158	0.95[JPT][hapmap]
rs7837582	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015355	chr8:112558586-113154605	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv539722	chr8:112558586-113154605	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1023006	chr8:112756497-113141033	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv539724	chr8:112756497-113141033	ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv533857	chr8:112819659-113801258	Enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv891320	chr8:112931908-113054458	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1460592	CSMD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:112976000-112978800	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr8:112976400-112977400	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr8:112976800-112977200	Enhancers	H1 Cell Line	embryonic stem cell
4	chr8:112976800-112977200	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr8:112977000-112977200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr8:112977000-112977400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr8:112977000-112977600	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr8:112977000-112978200	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr8:112977000-112978200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr8:112977000-112978600	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links