Variant report

Variant	rs11130526
Chromosome Location	chr3:56593893-56593894
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10222629	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1054092	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1054093	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130525	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130527	0.95[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes]
rs11712664	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11712799	0.83[EUR][1000 genomes]
rs11719707	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11719726	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13075010	0.83[CHB][hapmap]
rs1316647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13317989	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1388256	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1491170	0.85[YRI][hapmap]
rs1565378	0.82[EUR][1000 genomes]
rs17216657	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs17216685	0.81[CHB][hapmap];0.95[JPT][hapmap]
rs17216747	0.86[CHB][hapmap]
rs17235662	0.88[CEU][hapmap]
rs17235677	0.88[CEU][hapmap]
rs17235684	0.88[CEU][hapmap]
rs17288852	0.86[CHB][hapmap]
rs17825523	0.86[CEU][hapmap]
rs1812347	0.95[EUR][1000 genomes]
rs1873256	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2291498	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2291500	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2317132	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs282525	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs282530	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs282531	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs282535	0.84[YRI][hapmap]
rs282542	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3172355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3732505	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4681726	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4681904	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4681937	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4681955	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4682001	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4974221	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4974223	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4974225	0.91[EUR][1000 genomes]
rs55742226	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55828519	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55865922	0.85[ASN][1000 genomes]
rs55960262	0.87[ASN][1000 genomes]
rs56126040	0.85[ASN][1000 genomes]
rs56263252	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62251234	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62255964	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6445811	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6445812	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6556	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6764730	0.95[EUR][1000 genomes]
rs6767903	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6794450	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6799086	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7612464	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7620896	0.82[EUR][1000 genomes]
rs7628343	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7633478	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7635349	0.84[YRI][hapmap]
rs7641898	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7645941	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7647095	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7648297	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7649872	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9311609	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9311612	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs953540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9809117	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9814014	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs9816100	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9816265	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9819952	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9826788	0.85[ASN][1000 genomes]
rs9830377	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9834239	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9835134	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9841851	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9847362	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9861577	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9864701	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9867302	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9868059	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9871265	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9872059	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9881152	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9883842	0.85[EUR][1000 genomes];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	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11130526	CCDC66	cis	multi-tissue	Pritchard
rs11130526	CCDC66	cis	Whole Blood	GTEx
rs11130526	CCDC66	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56591800-56596000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:56591800-56599800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:56592000-56615600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:56592200-56609400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:56592400-56594000	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr3:56592400-56594000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr3:56592400-56594000	Weak transcription	Fetal Thymus	thymus
8	chr3:56592400-56594200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:56592400-56594600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:56592400-56594800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:56592400-56594800	Weak transcription	HSMM	muscle
12	chr3:56592400-56596000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr3:56592400-56596000	Weak transcription	Fetal Stomach	stomach
14	chr3:56592400-56596800	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:56592400-56599800	Weak transcription	Fetal Lung	lung
16	chr3:56592400-56600000	Weak transcription	Ovary	ovary
17	chr3:56592400-56601200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:56592400-56601400	Weak transcription	Left Ventricle	heart
19	chr3:56592400-56601800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:56592400-56601800	Weak transcription	Lung	lung
21	chr3:56592400-56602000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:56592400-56602800	Weak transcription	Esophagus	oesophagus
23	chr3:56592400-56602800	Weak transcription	Gastric	stomach
24	chr3:56592400-56602800	Weak transcription	Spleen	Spleen
25	chr3:56592400-56603000	Weak transcription	Pancreas	Pancrea
26	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
27	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
29	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
30	chr3:56592600-56594200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:56592600-56594200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:56592600-56594200	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr3:56592600-56594200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:56592600-56594200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr3:56592600-56594400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr3:56592600-56594600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:56592600-56594600	Weak transcription	Osteobl	bone
38	chr3:56592600-56594800	Weak transcription	Liver	Liver
39	chr3:56592600-56594800	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:56592600-56595600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:56592600-56595800	Weak transcription	Stomach Smooth Muscle	stomach
42	chr3:56592600-56596000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr3:56592600-56596000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:56592600-56598600	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:56592600-56598800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:56592600-56599600	Weak transcription	Thymus	Thymus
47	chr3:56592600-56600000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr3:56592600-56600000	Weak transcription	Colonic Mucosa	Colon
49	chr3:56592600-56600200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:56592600-56600200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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