Variant report

Variant	rs6601513
Chromosome Location	chr8:10594843-10594844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:10582500..10584094-chr8:10592919..10595783,2	K562	blood:
2	chr8:10581535..10584414-chr8:10592948..10594895,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10089615	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs10091386	0.84[CEU][hapmap]
rs10093774	0.84[CEU][hapmap];0.80[GIH][hapmap];0.85[TSI][hapmap]
rs10097283	0.82[CHB][hapmap]
rs10098699	0.92[CEU][hapmap]
rs10099021	0.85[CHD][hapmap]
rs10100209	0.80[CEU][hapmap];0.85[EUR][1000 genomes]
rs10100265	0.80[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap]
rs10100333	0.88[EUR][1000 genomes]
rs10105487	0.89[JPT][hapmap]
rs10107180	0.87[CHD][hapmap]
rs10113332	0.85[CHD][hapmap]
rs10481451	0.92[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs1073913	0.83[ASN][1000 genomes]
rs10903330	0.85[JPT][hapmap];0.87[TSI][hapmap]
rs1115866	0.90[CHB][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap]
rs1124010	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11250073	0.80[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs11250074	0.90[CHB][hapmap];0.90[JPT][hapmap]
rs11250076	0.87[YRI][hapmap]
rs11250077	0.92[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs12542888	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs12676417	0.82[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs13276026	0.81[ASN][1000 genomes]
rs1897207	0.81[ASN][1000 genomes]
rs1968400	0.83[ASN][1000 genomes]
rs1968401	0.83[ASN][1000 genomes]
rs1991651	0.91[ASW][hapmap];0.84[CEU][hapmap];0.85[TSI][hapmap]
rs2033369	0.82[CHB][hapmap]
rs2116093	0.82[ASN][1000 genomes]
rs2116095	0.91[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2277130	0.92[CEU][hapmap]
rs2409663	0.90[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap]
rs2409669	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.81[ASN][1000 genomes]
rs2409672	0.98[ASN][1000 genomes]
rs2409674	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2409675	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2898248	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2898251	0.82[ASN][1000 genomes]
rs3808603	0.84[CEU][hapmap]
rs4240670	0.88[JPT][hapmap]
rs4321967	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap]
rs4504595	0.94[CEU][hapmap]
rs4840512	0.98[ASN][1000 genomes]
rs4840513	0.83[ASN][1000 genomes]
rs4840516	0.96[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs4840517	0.85[JPT][hapmap]
rs4841434	0.85[EUR][1000 genomes]
rs4841436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4841437	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4841452	0.91[CEU][hapmap];0.91[YRI][hapmap]
rs57076989	0.84[ASN][1000 genomes]
rs6601512	0.80[EUR][1000 genomes]
rs6601521	0.86[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs6601522	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.87[TSI][hapmap];0.87[YRI][hapmap];0.81[ASN][1000 genomes]
rs6601523	0.91[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.84[JPT][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.80[ASN][1000 genomes]
rs6601525	0.93[CHD][hapmap]
rs6601529	0.92[CEU][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs6601530	0.85[JPT][hapmap]
rs6601536	0.80[CEU][hapmap]
rs6980805	0.92[CEU][hapmap]
rs6984744	0.81[ASN][1000 genomes]
rs6985218	0.83[CHD][hapmap]
rs6989160	0.84[CEU][hapmap]
rs6989370	0.82[ASN][1000 genomes]
rs6993841	0.80[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap]
rs7002117	0.83[ASN][1000 genomes]
rs7002282	0.92[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs7005905	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[EUR][1000 genomes]
rs7007318	0.89[EUR][1000 genomes]
rs718741	0.83[ASN][1000 genomes]
rs718742	0.82[ASN][1000 genomes]
rs752446	0.86[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs765658	0.84[ASN][1000 genomes]
rs7814757	0.92[CEU][hapmap]
rs7818181	0.80[CEU][hapmap]
rs7826180	0.90[CHD][hapmap]
rs7826189	0.92[CHD][hapmap]
rs7826458	0.88[CHD][hapmap]
rs7830431	0.92[CEU][hapmap]
rs7833945	0.84[CEU][hapmap]
rs7834466	0.90[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap]
rs7836366	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs9329231	0.82[ASN][1000 genomes]
rs9969626	0.92[CEU][hapmap];0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022994	chr8:10190618-10660122	Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv539466	chr8:10190618-10660122	Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	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
4	nsv1015932	chr8:10357101-10597856	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1022582	chr8:10571218-10636162	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv539468	chr8:10571218-10636162	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1026802	chr8:10576444-10754489	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
8	nsv539469	chr8:10576444-10754489	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
9	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
10	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6601513	MFHAS1	cis	cerebellum	SCAN
rs6601513	CLDN23	cis	multi-tissue	Pritchard
rs6601513	CTSB	cis	cerebellum	SCAN
rs6601513	FLJ10661	cis	cerebellum	SCAN
rs6601513	TDH	cis	cerebellum	SCAN
rs6601513	PRSS55	cis	cerebellum	SCAN
rs6601513	DEFB136	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:10594600-10595000	Enhancers	NHEK	skin
2	chr8:10594800-10598800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links