Variant report

Variant	rs4625466
Chromosome Location	chr11:9395649-9395650
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9394586..9396776-chr11:9404549..9406653,2	K562	blood:
2	chr11:9384654..9388171-chr11:9393379..9396078,3	MCF-7	breast:
3	chr11:9394195..9396569-chr11:9481524..9484200,3	K562	blood:

Variant related genes	Relation type
ENSG00000205339	Chromatin interaction
ENSG00000268403	Chromatin interaction
ENSG00000166478	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1020621	0.95[JPT][hapmap]
rs10437595	0.83[ASN][1000 genomes]
rs10437665	1.00[CHB][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs10770024	1.00[ASN][1000 genomes]
rs10770028	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs10770032	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs10840218	0.83[ASN][1000 genomes]
rs10840219	0.87[ASN][1000 genomes]
rs10840222	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10840224	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10840228	0.83[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap]
rs10840234	0.83[JPT][hapmap]
rs10840235	0.90[JPT][hapmap]
rs10840243	0.90[JPT][hapmap]
rs10840245	0.90[JPT][hapmap]
rs10840253	0.82[JPT][hapmap]
rs11042311	0.81[ASN][1000 genomes]
rs11042328	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs11042329	0.86[JPT][hapmap]
rs11042366	0.95[JPT][hapmap]
rs11042395	0.90[JPT][hapmap]
rs12291369	0.80[ASN][1000 genomes]
rs12795344	0.83[CHD][hapmap];0.95[JPT][hapmap]
rs2278900	0.90[JPT][hapmap]
rs2290423	0.90[JPT][hapmap]
rs2290424	0.90[JPT][hapmap]
rs2290425	0.90[JPT][hapmap]
rs35484677	0.83[ASN][1000 genomes]
rs41369549	0.95[JPT][hapmap]
rs4243948	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4362147	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4409822	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4471419	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4525241	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4575271	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4582976	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4810	0.95[JPT][hapmap]
rs4910046	0.81[ASN][1000 genomes]
rs4910047	0.81[ASN][1000 genomes]
rs4910048	1.00[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs4910049	0.82[ASN][1000 genomes]
rs4910053	0.90[JPT][hapmap]
rs4910459	0.85[ASN][1000 genomes]
rs4910460	0.85[ASN][1000 genomes]
rs4910461	0.84[ASN][1000 genomes]
rs6486307	0.95[JPT][hapmap]
rs6486361	0.95[JPT][hapmap]
rs6486394	0.90[JPT][hapmap]
rs7103038	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7104568	0.95[JPT][hapmap]
rs7105373	0.84[ASN][1000 genomes]
rs7115821	0.84[ASN][1000 genomes]
rs7122252	0.95[JPT][hapmap]
rs723297	0.90[JPT][hapmap]
rs727405	0.90[JPT][hapmap]
rs729313	0.90[JPT][hapmap]
rs7394742	0.83[ASN][1000 genomes]
rs7395630	0.83[ASN][1000 genomes]
rs7926589	0.90[JPT][hapmap]
rs7927350	0.90[JPT][hapmap]
rs7930205	0.96[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7944535	0.85[ASN][1000 genomes]
rs7944578	0.90[JPT][hapmap]
rs7946263	0.87[ASN][1000 genomes]
rs7949053	0.85[ASN][1000 genomes]
rs7952145	0.83[ASN][1000 genomes]
rs8785	0.94[JPT][hapmap]
rs972594	0.90[JPT][hapmap]
rs9971433	0.84[ASN][1000 genomes]
rs9971484	0.81[ASN][1000 genomes]

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	nsv916534	chr11:9188436-9516241	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1055078	chr11:9252857-9538877	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv508617	chr11:9314027-9408562	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4625466	HS2ST1	trans	cerebellum	SCAN
rs4625466	MRPL17	cis	cerebellum	SCAN
rs4625466	OR56A1	cis	cerebellum	SCAN
rs4625466	WEE1	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9386800-9406000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:9394800-9400600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr11:9394800-9400600	Weak transcription	HepG2	liver
4	chr11:9394800-9402000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:9395000-9400600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr11:9395000-9400600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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