Variant report

Variant	rs11130527
Chromosome Location	chr3:56610117-56610118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 100 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10222629	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs1054092	0.86[EUR][1000 genomes]
rs1054093	0.86[EUR][1000 genomes]
rs11130525	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes]
rs11130526	0.95[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs11712664	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs11712799	0.87[EUR][1000 genomes]
rs11719707	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes]
rs11719726	0.92[EUR][1000 genomes]
rs1316647	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs13317989	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs1388256	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1565378	0.86[EUR][1000 genomes]
rs17216685	0.85[JPT][hapmap]
rs1812347	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1873256	0.86[EUR][1000 genomes]
rs2291498	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes]
rs2291500	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2317132	0.97[EUR][1000 genomes]
rs282525	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs282530	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs282531	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs282542	0.98[EUR][1000 genomes]
rs3172355	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs3732505	0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs4681726	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs4681736	0.84[EUR][1000 genomes]
rs4681903	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs4681937	0.95[EUR][1000 genomes]
rs4681955	0.89[EUR][1000 genomes]
rs4682001	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs4682002	0.84[EUR][1000 genomes]
rs4974221	0.80[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4974223	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4974225	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55742226	0.92[EUR][1000 genomes]
rs55828519	0.86[EUR][1000 genomes]
rs56006703	0.83[ASN][1000 genomes]
rs56172256	0.82[EUR][1000 genomes]
rs56263252	0.94[EUR][1000 genomes]
rs62251234	0.85[EUR][1000 genomes]
rs62255964	0.92[EUR][1000 genomes]
rs6445811	0.89[EUR][1000 genomes]
rs6445812	0.89[EUR][1000 genomes]
rs6556	0.85[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs6764730	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6767903	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs6794450	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs6799086	0.91[EUR][1000 genomes]
rs7612464	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs7620896	0.86[EUR][1000 genomes]
rs7628343	0.94[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7633478	0.86[EUR][1000 genomes]
rs7641898	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7645941	0.86[EUR][1000 genomes]
rs7647095	0.86[EUR][1000 genomes]
rs7648297	0.86[EUR][1000 genomes]
rs7649872	0.86[EUR][1000 genomes]
rs873840	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9311609	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs9311612	0.86[EUR][1000 genomes]
rs953540	0.95[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes]
rs9809117	0.86[EUR][1000 genomes]
rs9814014	0.85[JPT][hapmap]
rs9816100	0.89[EUR][1000 genomes]
rs9816265	0.89[EUR][1000 genomes]
rs9819952	0.86[EUR][1000 genomes]
rs9830377	0.86[EUR][1000 genomes]
rs9834239	0.89[EUR][1000 genomes]
rs9835134	0.86[EUR][1000 genomes]
rs9841851	0.84[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs9847362	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs9861577	0.86[EUR][1000 genomes]
rs9864701	0.89[EUR][1000 genomes]
rs9867302	0.85[CEU][hapmap];0.89[JPT][hapmap];0.89[EUR][1000 genomes]
rs9868059	0.95[EUR][1000 genomes]
rs9871265	1.00[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9872059	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs9881152	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9883842	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347557	chr3:56466500-56619322	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv876817	chr3:56517253-56649282	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv460557	chr3:56594735-56661320	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv590362	chr3:56594735-56661320	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv822097	chr3:56607112-56620842	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv435762	chr3:56607518-56622066	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv19690	chr3:56607723-56621531	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv822099	chr3:56607804-56620842	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1827962	chr3:56607811-56617333	Weak transcription Active TSS ZNF genes & repeats Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1830828	chr3:56607811-56617333	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1832534	chr3:56607811-56617333	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv1831026	chr3:56607811-56620106	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv1832365	chr3:56607811-56620106	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv1826366	chr3:56607826-56620842	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	esv1830577	chr3:56607826-56620842	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv963260	chr3:56608026-56620152	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv1825630	chr3:56608033-56620106	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv1827186	chr3:56608033-56620106	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	esv1827416	chr3:56608033-56620106	Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv528087	chr3:56608033-56628031	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11130527	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs11130527	CCDC66	cis	Whole Blood	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
4	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
5	chr3:56592800-56610200	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr3:56592800-56644600	Weak transcription	Fetal Heart	heart
7	chr3:56593200-56616400	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:56594200-56610200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:56600600-56640000	Weak transcription	NHLF	lung
10	chr3:56601800-56615800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:56602400-56616200	Weak transcription	Dnd41	blood
12	chr3:56603000-56631600	Weak transcription	Fetal Brain Male	brain
13	chr3:56603200-56616600	Weak transcription	GM12878-XiMat	blood
14	chr3:56603200-56650400	Weak transcription	K562	blood
15	chr3:56603600-56612200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr3:56603600-56615800	Weak transcription	Gastric	stomach
17	chr3:56603600-56640000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:56603800-56615600	Weak transcription	Brain Germinal Matrix	brain
19	chr3:56604200-56615600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:56604200-56627600	Weak transcription	Brain Angular Gyrus	brain
21	chr3:56604600-56615800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:56604600-56624600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:56604600-56625000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr3:56604600-56625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr3:56604600-56627600	Weak transcription	HUVEC	blood vessel
26	chr3:56605600-56639600	Weak transcription	Pancreas	Pancrea
27	chr3:56605800-56615400	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:56605800-56639400	Weak transcription	Spleen	Spleen
29	chr3:56605800-56639600	Weak transcription	Esophagus	oesophagus
30	chr3:56606000-56611800	Weak transcription	Fetal Stomach	stomach
31	chr3:56606000-56615600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:56606000-56615800	Weak transcription	Aorta	Aorta
33	chr3:56606000-56617000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:56606000-56627600	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:56606000-56627600	Weak transcription	Left Ventricle	heart
36	chr3:56606000-56629200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:56606200-56650200	Weak transcription	Colonic Mucosa	Colon
38	chr3:56606600-56616400	Weak transcription	Placenta	Placenta
39	chr3:56606600-56617000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr3:56606600-56627800	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:56606800-56624000	Weak transcription	Brain Substantia Nigra	brain
42	chr3:56606800-56627600	Weak transcription	Osteobl	bone
43	chr3:56607000-56616400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:56607000-56624200	Weak transcription	HepG2	liver
45	chr3:56607000-56624400	Weak transcription	NH-A	brain
46	chr3:56607400-56616200	Weak transcription	Fetal Intestine Small	intestine
47	chr3:56607600-56615800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr3:56607600-56616400	Weak transcription	Hela-S3	cervix
49	chr3:56607600-56616600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:56607600-56616600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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