Variant report

Variant	rs62280669
Chromosome Location	chr3:101094256-101094257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10451923	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10511189	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1520654	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16843627	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16843634	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16843699	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16843817	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271972	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35902489	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3732893	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3773915	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3773917	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3773918	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4260407	0.91[EUR][1000 genomes]
rs4553955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280636	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62280637	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62280663	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280664	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280665	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62280670	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62280671	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280673	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280675	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62280719	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62280720	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62280721	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62280722	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62280725	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62280726	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62280728	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62280731	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62280733	0.92[EUR][1000 genomes]
rs62280735	0.92[EUR][1000 genomes]
rs62280737	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62280745	0.92[EUR][1000 genomes]
rs62280747	0.91[EUR][1000 genomes]
rs62282871	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62282873	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62282875	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62282885	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62282886	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62282887	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62282888	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62282889	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62282890	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62282892	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441595	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6796058	0.82[AMR][1000 genomes]
rs6798685	0.82[AMR][1000 genomes]
rs72932462	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7611378	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7621506	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7622461	0.92[EUR][1000 genomes]
rs7632064	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7634592	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9790303	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1003475	chr3:101005238-101120030	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101030800-101096400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:101038600-101101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:101039800-101106600	Weak transcription	Thymus	Thymus
4	chr3:101043200-101105000	Weak transcription	Brain Anterior Caudate	brain
5	chr3:101043800-101096600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:101044400-101103000	Weak transcription	Gastric	stomach
7	chr3:101045800-101110800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:101047400-101096000	Weak transcription	Psoas Muscle	Psoas
9	chr3:101049200-101096000	Weak transcription	Ovary	ovary
10	chr3:101049200-101102200	Weak transcription	Right Ventricle	heart
11	chr3:101066200-101095400	Weak transcription	Fetal Kidney	kidney
12	chr3:101066200-101096000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:101076200-101102000	Weak transcription	Lung	lung
14	chr3:101076200-101105600	Weak transcription	Esophagus	oesophagus
15	chr3:101076600-101096400	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:101077000-101095800	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:101077000-101096000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:101077000-101102200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr3:101077800-101094400	Weak transcription	Fetal Intestine Small	intestine
20	chr3:101077800-101096000	Weak transcription	Small Intestine	intestine
21	chr3:101077800-101101000	Weak transcription	NHDF-Ad	bronchial
22	chr3:101077800-101102000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:101079200-101096000	Weak transcription	HSMMtube	muscle
24	chr3:101079600-101094400	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:101080400-101098800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:101081200-101094600	Weak transcription	Stomach Mucosa	stomach
27	chr3:101083200-101102000	Weak transcription	Left Ventricle	heart
28	chr3:101083400-101101800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:101083400-101105200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:101083600-101094400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:101083600-101096400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:101083600-101098200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:101083800-101096000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:101084000-101094400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:101084400-101102000	Weak transcription	Fetal Stomach	stomach
36	chr3:101084600-101106600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:101084800-101102000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr3:101085000-101106600	Weak transcription	Fetal Brain Female	brain
39	chr3:101085400-101096200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:101085400-101098200	Weak transcription	Primary hematopoietic stem cells	blood
41	chr3:101085600-101094600	Weak transcription	Liver	Liver
42	chr3:101085600-101095200	Weak transcription	Fetal Heart	heart
43	chr3:101085600-101096000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:101085600-101096800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:101085600-101098600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:101085600-101098600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:101085600-101098800	Weak transcription	K562	blood
48	chr3:101085600-101106800	Weak transcription	Dnd41	blood
49	chr3:101085600-101137600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr3:101087600-101094600	Weak transcription	HepG2	liver

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