Variant report

Variant	rs11626496
Chromosome Location	chr14:65600981-65600982
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:65600572..65603233-chr14:65606608..65608580,2	MCF-7	breast:
2	chr14:65600313..65602525-chr14:65607232..65610149,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10873180	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10873181	0.85[EUR][1000 genomes]
rs10873182	0.85[EUR][1000 genomes]
rs10873183	0.84[EUR][1000 genomes]
rs10873185	0.83[EUR][1000 genomes]
rs11158572	0.90[ASN][1000 genomes]
rs11158573	0.90[ASN][1000 genomes]
rs11158574	0.85[CEU][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11158577	0.84[CEU][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11158578	0.85[EUR][1000 genomes]
rs11623603	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11625045	0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs11626156	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11627859	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12100605	0.87[EUR][1000 genomes]
rs12147959	0.87[ASN][1000 genomes]
rs12880781	0.82[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.90[ASN][1000 genomes]
rs12884836	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12887607	0.83[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12888794	0.88[ASN][1000 genomes]
rs17102423	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17825846	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1953228	0.88[ASN][1000 genomes]
rs2898863	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34062462	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35002541	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35176994	0.93[ASN][1000 genomes]
rs35769504	0.88[ASN][1000 genomes]
rs4902358	0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap]
rs4902363	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4902364	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902365	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902367	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55658675	0.88[ASN][1000 genomes]
rs61987428	0.85[EUR][1000 genomes]
rs61987429	0.85[EUR][1000 genomes]
rs7143495	0.82[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.85[ASN][1000 genomes]
rs7144259	0.94[JPT][hapmap]
rs7154852	0.88[ASN][1000 genomes]
rs7161394	0.82[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs762810	0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap]
rs8004805	0.95[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8009396	0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs8009714	0.90[ASN][1000 genomes]
rs8015330	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8018788	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8181937	0.88[ASN][1000 genomes]
rs8181938	0.88[ASN][1000 genomes]
rs8181939	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs868814	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs884683	0.82[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs942627	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832816	chr14:65473244-65644645	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
2	esv1833060	chr14:65594460-65607642	Enhancers Weak transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11626496	GPX2	cis	cerebellum	SCAN
rs11626496	RAB15	cis	lymphoblastoid	seeQTL
rs11626496	SIX4	cis	cerebellum	SCAN
rs11626496	WDR89	cis	cerebellum	SCAN
rs11626496	RAB15	cis	cerebellum	SCAN
rs11626496	MAX	cis	cerebellum	SCAN
rs11626496	MAX	cis	parietal	SCAN
rs11626496	CHRNA5	trans	cerebellum	SCAN
rs11626496	MAX	cis	multi-tissue	Pritchard
rs11626496	CHURC1	cis	multi-tissue	Pritchard

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65596800-65602600	Enhancers	Fetal Intestine Small	intestine
2	chr14:65597800-65602600	Enhancers	Fetal Intestine Large	intestine
3	chr14:65598200-65601400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr14:65598200-65601600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr14:65598200-65602200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr14:65598400-65601400	Weak transcription	HSMM	muscle
7	chr14:65598800-65601800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr14:65598800-65604400	Weak transcription	Colonic Mucosa	Colon
9	chr14:65598800-65604400	Weak transcription	Osteobl	bone
10	chr14:65599000-65601800	Weak transcription	NHEK	skin
11	chr14:65599200-65602000	Enhancers	HepG2	liver
12	chr14:65600800-65601000	Enhancers	Duodenum Mucosa	Duodenum
13	chr14:65600800-65601000	Enhancers	Rectal Mucosa Donor 29	rectum

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