Variant report

Variant	rs10975552
Chromosome Location	chr9:6351834-6351835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10115362	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10115883	0.89[JPT][hapmap]
rs10122116	0.94[JPT][hapmap]
rs10491836	0.87[YRI][hapmap]
rs10739094	0.84[AFR][1000 genomes]
rs10739097	0.83[EUR][1000 genomes]
rs10739098	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10739099	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10758783	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10758784	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10758785	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10758788	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10758789	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10758790	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs10815411	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10815412	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10815428	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10975553	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10975557	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10975583	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10975595	1.00[JPT][hapmap]
rs10975605	0.89[JPT][hapmap]
rs1156747	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11791651	0.88[JPT][hapmap]
rs11795355	0.89[JPT][hapmap]
rs12346455	0.89[JPT][hapmap]
rs12347573	0.88[JPT][hapmap]
rs12376117	0.84[ASN][1000 genomes]
rs1322171	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13283381	0.84[JPT][hapmap]
rs13291472	0.89[JPT][hapmap]
rs13298500	0.82[JPT][hapmap]
rs1381035	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs1575263	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1575264	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16924328	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs16924356	0.95[YRI][hapmap]
rs16924428	0.94[AFR][1000 genomes]
rs16924434	0.99[ASN][1000 genomes]
rs16924562	0.94[JPT][hapmap]
rs16924624	0.89[JPT][hapmap]
rs16924626	0.94[JPT][hapmap]
rs16924631	0.94[JPT][hapmap]
rs16924634	0.84[JPT][hapmap]
rs1870696	0.94[JPT][hapmap]
rs1903419	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1969731	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2169282	1.00[ASN][1000 genomes]
rs2169283	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs2169286	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs3739654	0.89[JPT][hapmap]
rs4740844	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4742181	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4742201	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4742202	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs59606381	0.94[AFR][1000 genomes]
rs6477087	0.89[JPT][hapmap]
rs67852216	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7022186	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7027505	0.81[AFR][1000 genomes]
rs7029772	0.83[JPT][hapmap]
rs7039175	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7039959	0.90[ASN][1000 genomes]
rs719724	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs719725	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7850988	0.84[AFR][1000 genomes]
rs7851246	0.94[AFR][1000 genomes]
rs7852539	0.89[JPT][hapmap]
rs7857628	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7860427	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7865955	0.94[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7875812	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	nsv948847	chr9:5712626-6417677	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
8	nsv1024324	chr9:6308178-6408875	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv1019222	chr9:6328242-6402856	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6342400-6352000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:6351000-6355800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:6351400-6352800	Enhancers	Hela-S3	cervix
4	chr9:6351800-6352200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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