Variant report

Variant	rs62255966
Chromosome Location	chr3:56594389-56594390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11130522	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1388252	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1491162	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1491167	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17216678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17216712	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17216754	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17288866	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17288873	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2306930	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2306931	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41276465	0.80[ASN][1000 genomes]
rs41276467	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs41276469	0.89[EUR][1000 genomes]
rs4292200	0.96[ASN][1000 genomes]
rs56758331	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57861120	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58457441	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59835031	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59897254	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60606369	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61456176	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61654248	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61747994	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs62249737	0.96[EUR][1000 genomes]
rs62251182	0.88[EUR][1000 genomes]
rs62251183	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251186	0.89[EUR][1000 genomes]
rs62251188	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251190	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251192	0.89[EUR][1000 genomes]
rs62251193	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251197	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251228	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251229	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251230	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251233	0.89[EUR][1000 genomes]
rs62251235	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251238	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251239	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251241	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251244	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62251245	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62254329	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255965	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62255967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62255969	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62255970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62255971	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62255972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62255973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62255974	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62255977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62255978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62255980	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62255981	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256011	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256013	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256014	0.96[EUR][1000 genomes]
rs62256017	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256018	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256019	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256020	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256022	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62256023	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6782254	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6788512	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6802548	0.89[EUR][1000 genomes]
rs6810125	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73075746	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73081816	0.88[EUR][1000 genomes]
rs73081836	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73081850	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73083715	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73083725	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7635945	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs955247	0.83[AMR][1000 genomes];0.96[EUR][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

No data

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	chr3:56592400-56594600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr3:56592400-56594800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:56592400-56594800	Weak transcription	HSMM	muscle
8	chr3:56592400-56596000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:56592400-56596000	Weak transcription	Fetal Stomach	stomach
10	chr3:56592400-56596800	Weak transcription	Fetal Muscle Leg	muscle
11	chr3:56592400-56599800	Weak transcription	Fetal Lung	lung
12	chr3:56592400-56600000	Weak transcription	Ovary	ovary
13	chr3:56592400-56601200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:56592400-56601400	Weak transcription	Left Ventricle	heart
15	chr3:56592400-56601800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:56592400-56601800	Weak transcription	Lung	lung
17	chr3:56592400-56602000	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:56592400-56602800	Weak transcription	Esophagus	oesophagus
19	chr3:56592400-56602800	Weak transcription	Gastric	stomach
20	chr3:56592400-56602800	Weak transcription	Spleen	Spleen
21	chr3:56592400-56603000	Weak transcription	Pancreas	Pancrea
22	chr3:56592400-56607400	Weak transcription	Psoas Muscle	Psoas
23	chr3:56592400-56615600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr3:56592400-56639800	Weak transcription	Right Ventricle	heart
25	chr3:56592400-56644800	Weak transcription	Small Intestine	intestine
26	chr3:56592600-56594400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:56592600-56594600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr3:56592600-56594600	Weak transcription	Osteobl	bone
29	chr3:56592600-56594800	Weak transcription	Liver	Liver
30	chr3:56592600-56594800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:56592600-56595600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr3:56592600-56595800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:56592600-56596000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:56592600-56596000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:56592600-56598600	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:56592600-56598800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:56592600-56599600	Weak transcription	Thymus	Thymus
38	chr3:56592600-56600000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:56592600-56600000	Weak transcription	Colonic Mucosa	Colon
40	chr3:56592600-56600200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:56592600-56600200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:56592600-56600200	Weak transcription	NHLF	lung
43	chr3:56592600-56601000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr3:56592600-56601000	Weak transcription	HSMMtube	muscle
45	chr3:56592600-56601800	Weak transcription	Aorta	Aorta
46	chr3:56592600-56602200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr3:56592600-56602200	Weak transcription	Brain Germinal Matrix	brain
48	chr3:56592600-56602200	Weak transcription	Fetal Brain Male	brain
49	chr3:56592600-56603000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:56592600-56603800	Weak transcription	Stomach Mucosa	stomach

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