Variant report

Variant	rs6959861
Chromosome Location	chr7:48479836-48479837
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10227179	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10227187	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10230786	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10237159	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10237473	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10238373	0.94[JPT][hapmap]
rs10248546	0.94[JPT][hapmap]
rs10249009	1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10249279	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10251517	1.00[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10255612	1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10256255	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10267753	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10268515	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10273407	0.94[JPT][hapmap];0.81[MEX][hapmap];0.80[AMR][1000 genomes]
rs10276131	0.88[JPT][hapmap];0.81[AMR][1000 genomes]
rs10276989	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10277088	0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs10280481	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10282413	0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs11762388	0.94[JPT][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes]
rs11765338	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11765607	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11766842	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11770110	0.88[JPT][hapmap];0.95[MEX][hapmap]
rs11771470	0.81[AMR][1000 genomes]
rs11772033	0.84[AMR][1000 genomes]
rs11981491	0.84[AMR][1000 genomes]
rs12533158	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12533748	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12535273	0.94[JPT][hapmap]
rs12535354	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12537664	0.94[JPT][hapmap]
rs12540368	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1433499	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1433500	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1534393	0.94[JPT][hapmap]
rs17132342	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17132359	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17662893	0.80[AMR][1000 genomes]
rs17730186	0.94[JPT][hapmap];0.84[AMR][1000 genomes]
rs1836092	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1881077	0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs1881079	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1881080	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1918579	0.84[AMR][1000 genomes]
rs2043391	0.84[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2043392	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2043393	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2043394	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2178088	0.94[JPT][hapmap]
rs2885482	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35345934	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4022347	0.84[AMR][1000 genomes]
rs4144065	0.94[JPT][hapmap];0.81[MEX][hapmap];0.84[AMR][1000 genomes]
rs4256548	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4621756	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4623358	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4642585	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4917019	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4917020	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4917140	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4917141	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4917142	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4917143	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4917144	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4917145	0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4917146	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4917147	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4917148	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4917149	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4917152	1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4917153	1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4917154	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4917155	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56395407	0.80[AMR][1000 genomes]
rs58343601	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58713664	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59698723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59915104	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs67312973	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67563133	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73105511	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73107511	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs73107532	0.82[AMR][1000 genomes]
rs73107543	0.84[AMR][1000 genomes]
rs73111420	0.80[AMR][1000 genomes]
rs735069	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs735070	0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7782619	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7789206	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7799302	0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs7808037	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817336	chr7:48238233-48563988	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1022980	chr7:48243227-48567060	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv538833	chr7:48243227-48567060	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1022578	chr7:48244414-48584664	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1023575	chr7:48244414-48586685	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1015183	chr7:48244414-48588598	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1032221	chr7:48302789-48546684	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv533811	chr7:48313757-48482470	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1015399	chr7:48321542-48544359	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv2761325	chr7:48409639-48557382	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv888006	chr7:48467581-48491825	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv888007	chr7:48467581-48533508	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv524173	chr7:48479620-48479836	Strong transcription Weak transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6959861	CCM2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48468000-48500000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr7:48469200-48480200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:48479400-48483400	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links