Variant report

Variant	rs11936946
Chromosome Location	chr4:92012047-92012048
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	chr10:82295674..82298297-chr4:92009865..92012633,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226659	Chromatin interaction
ENSG00000178217	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10023583	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10029387	0.91[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs11936423	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11938021	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12508842	0.89[CEU][hapmap]
rs12510441	0.89[CEU][hapmap]
rs13105627	0.89[CEU][hapmap]
rs13115351	0.89[CEU][hapmap]
rs1544385	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs17182898	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17183429	0.85[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.88[TSI][hapmap];0.93[ASN][1000 genomes]
rs17243008	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap]
rs2107007	0.89[CEU][hapmap]
rs2189186	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2214384	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214385	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs2214387	0.86[ASN][1000 genomes]
rs34365518	0.82[ASN][1000 genomes]
rs35223253	0.82[ASN][1000 genomes]
rs3944131	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4302434	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4635787	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4693258	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4693262	0.85[CHB][hapmap]
rs55871997	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56091462	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59017289	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61117447	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62312188	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62312189	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62312245	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6532280	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs67816799	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6842062	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs714186	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap]
rs7655384	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[JPT][hapmap]
rs7677433	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[TSI][hapmap]
rs7688333	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs7697891	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491945	chr4:91753638-92240582	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv879559	chr4:91918870-92152678	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv869023	chr4:91940838-92935383	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2757943	chr4:91946664-92146114	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2759267	chr4:91946664-92146114	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1831682	chr4:91979094-92114281	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv528519	chr4:92005403-92017500	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv879561	chr4:92005403-92061748	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	esv3448147	chr4:92011533-92275731	Active TSS Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11936946	ATOH1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:92009400-92017200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr4:92010800-92014400	Weak transcription	Esophagus	oesophagus
3	chr4:92011600-92012600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links