Variant report

Variant	rs6877524
Chromosome Location	chr5:112660029-112660030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10042223	0.88[YRI][hapmap]
rs10051834	0.91[YRI][hapmap]
rs10062004	0.87[YRI][hapmap]
rs10074214	0.88[YRI][hapmap]
rs10077020	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10428666	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs10519343	0.83[GIH][hapmap];0.95[MEX][hapmap]
rs10519346	0.83[GIH][hapmap];0.95[MEX][hapmap]
rs10900685	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[YRI][hapmap]
rs1116547	0.85[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11241197	0.81[AMR][1000 genomes]
rs11241201	0.84[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11241206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[YRI][hapmap];0.86[ASN][1000 genomes]
rs11738075	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs11738215	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs11740353	0.83[GIH][hapmap];0.95[MEX][hapmap]
rs11741937	0.80[AMR][1000 genomes]
rs11748465	0.83[GIH][hapmap];0.95[MEX][hapmap]
rs11748503	0.90[ASN][1000 genomes]
rs11748524	0.83[GIH][hapmap];0.95[MEX][hapmap]
rs12188069	0.83[GIH][hapmap];0.90[MEX][hapmap]
rs12514091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12516418	0.86[JPT][hapmap];0.91[YRI][hapmap]
rs12519753	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12520003	1.00[CHB][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12521391	0.83[GIH][hapmap];0.90[MEX][hapmap]
rs12522862	0.83[GIH][hapmap];0.90[MEX][hapmap]
rs12523027	0.81[AMR][1000 genomes]
rs12523255	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[ASN][1000 genomes]
rs13188946	0.88[YRI][hapmap]
rs13360719	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1366393	0.88[YRI][hapmap]
rs1443683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517209	0.86[ASN][1000 genomes]
rs1586943	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17135463	0.83[GIH][hapmap];0.90[MEX][hapmap]
rs17135515	0.83[GIH][hapmap];0.95[MEX][hapmap]
rs17135526	0.83[GIH][hapmap];0.95[MEX][hapmap]
rs17135534	0.86[MEX][hapmap]
rs17135597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17135608	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[ASN][1000 genomes]
rs17135616	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17135630	0.86[JPT][hapmap]
rs1833678	1.00[JPT][hapmap]
rs1838208	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850407	0.88[YRI][hapmap]
rs1850410	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1850412	0.88[YRI][hapmap]
rs1997521	0.90[MEX][hapmap]
rs2068923	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2222144	0.88[YRI][hapmap]
rs26959	0.92[YRI][hapmap]
rs26961	0.91[YRI][hapmap]
rs26966	0.91[YRI][hapmap]
rs27567	0.92[YRI][hapmap]
rs3846721	1.00[JPT][hapmap]
rs3846722	0.88[JPT][hapmap]
rs4331889	0.84[YRI][hapmap]
rs4705551	0.88[JPT][hapmap]
rs4705814	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[ASN][1000 genomes]
rs4705817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4705818	0.84[ASN][1000 genomes]
rs4705819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs59954246	0.80[AFR][1000 genomes]
rs62374372	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6594701	0.91[YRI][hapmap]
rs6594703	0.95[YRI][hapmap]
rs6594704	0.92[YRI][hapmap]
rs6594705	0.92[YRI][hapmap]
rs6594707	0.84[YRI][hapmap]
rs6594710	0.88[YRI][hapmap]
rs6594712	0.88[YRI][hapmap]
rs66728961	0.86[ASN][1000 genomes]
rs67764628	0.82[ASN][1000 genomes]
rs6864528	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[YRI][hapmap];0.84[ASN][1000 genomes]
rs6867397	0.88[YRI][hapmap]
rs6878001	0.88[JPT][hapmap]
rs6879800	0.88[JPT][hapmap];0.81[MEX][hapmap]
rs6883441	0.88[JPT][hapmap]
rs6887565	0.90[MEX][hapmap]
rs6894687	0.84[YRI][hapmap]
rs73236478	0.84[ASN][1000 genomes]
rs73246681	0.80[AMR][1000 genomes]
rs7707443	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs7708084	0.90[YRI][hapmap]
rs7717000	0.88[JPT][hapmap];0.87[YRI][hapmap]
rs7717422	0.88[YRI][hapmap]
rs7725589	0.91[YRI][hapmap]
rs9326886	0.87[YRI][hapmap]
rs9326887	0.90[YRI][hapmap]
rs9326888	0.88[YRI][hapmap]
rs957777	1.00[JPT][hapmap]
rs9632462	0.84[YRI][hapmap]
rs971370	0.86[MEX][hapmap]
rs971371	0.86[MEX][hapmap]
rs977997	0.86[MEX][hapmap]
rs9800316	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112648800-112666600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:112653000-112673600	Weak transcription	Fetal Kidney	kidney
3	chr5:112656000-112666200	Weak transcription	HMEC	breast
4	chr5:112656200-112661200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:112656600-112666600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:112657400-112669200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:112657600-112660600	Weak transcription	Liver	Liver
8	chr5:112658000-112666600	Weak transcription	Left Ventricle	heart

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