Variant report

Variant	rs556730
Chromosome Location	chr11:63142877-63142878
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	chr11:63136269..63139132-chr11:63142278..63145159,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149742	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10750998	0.99[ASN][1000 genomes]
rs10792406	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs10897383	0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs10897384	0.91[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs10897396	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap]
rs10897397	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap]
rs10897399	0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs10897407	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs11231397	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11231409	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11231410	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11231411	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs11231412	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11231413	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1152244	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11605137	0.97[ASN][1000 genomes]
rs1193726	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1193733	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1193786	0.86[ASN][1000 genomes]
rs1193787	0.90[ASN][1000 genomes]
rs1193891	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs1193892	0.95[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap]
rs1201559	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs12283500	0.96[ASN][1000 genomes]
rs12293171	0.90[ASN][1000 genomes]
rs12574223	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1300798	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1404608	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1525064	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs1525071	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs1723219	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1790218	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs1790226	0.90[ASN][1000 genomes]
rs1944086	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2317089	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2510590	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2958546	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3891629	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs3915142	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4121881	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4445638	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap]
rs471044	0.94[ASN][1000 genomes]
rs474096	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs474874	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs483012	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs486460	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs488803	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs494608	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4963385	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap]
rs4963405	0.97[ASN][1000 genomes]
rs499003	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs502642	0.96[ASN][1000 genomes]
rs505653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs510547	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511480	0.99[ASN][1000 genomes]
rs513338	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs515213	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs516536	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs517655	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs526686	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs532085	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap]
rs534799	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap]
rs538309	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs543429	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs549144	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs557658	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap]
rs557879	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs558472	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs563948	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs564917	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs566456	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs575009	1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6591778	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs688999	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7126435	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs722508	1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap]
rs7949840	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]

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	nsv1051171	chr11:62987064-63835715	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
2	nsv1053585	chr11:63057767-63180308	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv555178	chr11:63078742-63197930	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs556730	ACTN3	cis	cerebellum	SCAN
rs556730	EFEMP2	cis	parietal	SCAN
rs556730	CD6	cis	cerebellum	SCAN
rs556730	TMEM109	cis	parietal	SCAN
rs556730	TMEM179B	cis	parietal	SCAN
rs556730	TSGA10IP	cis	parietal	SCAN
rs556730	SDHAF2	cis	parietal	SCAN
rs556730	DNAJC4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:63141400-63153200	Weak transcription	HepG2	liver
2	chr11:63142400-63143200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr11:63142600-63147000	Strong transcription	Liver	Liver
4	chr11:63142800-63143000	Bivalent/Poised TSS	Small Intestine	intestine

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