Variant report

Variant	rs6592510
Chromosome Location	chr11:72788823-72788824
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11235620	0.83[CEU][hapmap]
rs11822039	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12294037	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12419915	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12808517	0.91[CEU][hapmap]
rs1612659	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1783575	0.93[ASW][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs2187494	0.82[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs2366256	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3862796	1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs4394861	0.87[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4400839	0.83[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs4944016	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4944823	0.96[ASN][1000 genomes]
rs593753	1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs6592500	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6592505	0.91[CEU][hapmap];0.93[GIH][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes]
rs6592509	0.91[CEU][hapmap];0.93[GIH][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7102253	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7108955	1.00[CEU][hapmap]
rs7124723	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[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	esv2422418	chr11:72646518-72807865	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv555411	chr11:72647296-72800970	Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6592510	ATG16L2	cis	parietal	SCAN
rs6592510	FGF4	cis	cerebellum	SCAN
rs6592510	STARD10	cis	Whole Blood	GTEx
rs6592510	KCNE3	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:72746600-72824600	Weak transcription	Thymus	Thymus
2	chr11:72764200-72824600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:72768800-72797000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr11:72771600-72799400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr11:72773000-72810800	Weak transcription	Fetal Stomach	stomach
6	chr11:72773400-72791000	Weak transcription	Fetal Thymus	thymus
7	chr11:72773400-72810400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr11:72782600-72825200	Weak transcription	Lung	lung
9	chr11:72783200-72798800	Weak transcription	Left Ventricle	heart
10	chr11:72784200-72797800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr11:72784200-72798800	Weak transcription	Right Ventricle	heart
12	chr11:72784200-72799000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr11:72784400-72789200	Weak transcription	HSMMtube	muscle
14	chr11:72784400-72789600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr11:72784400-72797800	Weak transcription	Brain Substantia Nigra	brain
16	chr11:72784400-72806400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr11:72784600-72789600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:72784600-72794800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr11:72784600-72795000	Weak transcription	HMEC	breast
20	chr11:72784600-72796200	Weak transcription	Ovary	ovary
21	chr11:72784600-72798000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr11:72784600-72798800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:72784600-72799000	Weak transcription	Hela-S3	cervix
24	chr11:72784600-72806400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:72784600-72810800	Weak transcription	Aorta	Aorta
26	chr11:72784600-72812000	Weak transcription	NHEK	skin
27	chr11:72784800-72795600	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr11:72785000-72796400	Weak transcription	Brain Angular Gyrus	brain
29	chr11:72785000-72811000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr11:72785200-72806600	Weak transcription	Osteobl	bone
31	chr11:72785200-72810600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr11:72786000-72789200	Weak transcription	Fetal Intestine Small	intestine
33	chr11:72786000-72804600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr11:72786200-72823600	Weak transcription	Placenta	Placenta
35	chr11:72786400-72789000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr11:72786400-72796400	Weak transcription	HepG2	liver
37	chr11:72786600-72793200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr11:72786600-72798800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr11:72787200-72790400	Strong transcription	Primary B cells from peripheral blood	blood
40	chr11:72788200-72825400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:72788400-72789000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr11:72788400-72789000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
43	chr11:72788400-72789000	ZNF genes & repeats	Fetal Kidney	kidney
44	chr11:72788400-72789000	ZNF genes & repeats	HUVEC	blood vessel
45	chr11:72788400-72789200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr11:72788400-72789200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr11:72788400-72789200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
48	chr11:72788400-72789200	ZNF genes & repeats	Adipose Nuclei	Adipose
49	chr11:72788400-72789200	ZNF genes & repeats	Fetal Heart	heart
50	chr11:72788400-72789400	ZNF genes & repeats	Primary B cells from cord blood	blood

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