Variant report

Variant	rs740509
Chromosome Location	chr7:39388947-39388948
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:49416978..49419812-chr7:39387654..39389957,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10248165	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs10251013	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10269183	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs11971775	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12701728	0.84[JPT][hapmap]
rs12701729	0.86[JPT][hapmap]
rs1558159	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1990243	0.82[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs2190887	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237411	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299135	0.88[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2299137	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299140	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2299141	1.00[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329388	1.00[CEU][hapmap];0.88[CHB][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329389	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329390	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2329391	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2876835	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3800854	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60586729	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6962623	0.88[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.96[ASN][1000 genomes]
rs887013	0.85[ASN][1000 genomes]
rs917401	0.81[ASN][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	nsv1015572	chr7:39185895-39413053	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv538821	chr7:39185895-39413053	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv887969	chr7:39265429-39391875	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs740509	C7orf10	cis	brain	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39383400-39391800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr7:39383600-39391200	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr7:39388000-39389600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr7:39388800-39389600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr7:39388800-39389600	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr7:39388800-39389600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:39388800-39389600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links