Variant report

Variant	rs2420065
Chromosome Location	chr10:116583753-116583754
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 136 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:131)

rs_ID	r²[population]
rs1046492	0.89[AFR][1000 genomes]
rs10490908	0.89[AFR][1000 genomes]
rs10490909	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10885613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885614	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885615	0.80[ASN][1000 genomes]
rs10885616	0.80[ASN][1000 genomes]
rs10885618	0.90[EUR][1000 genomes]
rs10885620	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10885621	0.81[ASN][1000 genomes]
rs10885622	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196924	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11196925	0.81[ASN][1000 genomes]
rs11196926	0.81[ASN][1000 genomes]
rs11196929	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196930	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196931	0.81[ASN][1000 genomes]
rs11196932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196935	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11196936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196940	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196941	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196942	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11196943	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196944	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196945	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196946	0.81[ASN][1000 genomes]
rs11196947	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196948	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196950	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11196951	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196952	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196953	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196954	0.80[ASN][1000 genomes]
rs11196955	0.80[ASN][1000 genomes]
rs11196956	0.80[ASN][1000 genomes]
rs11196957	0.80[ASN][1000 genomes]
rs11196959	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11196962	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11818115	0.88[AFR][1000 genomes]
rs11819372	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12218498	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12411629	0.80[ASN][1000 genomes]
rs12414613	0.80[ASN][1000 genomes]
rs12415173	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12765350	0.88[AFR][1000 genomes]
rs12773943	0.88[AFR][1000 genomes]
rs1359079	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359080	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17092480	0.81[ASN][1000 genomes]
rs17092491	0.81[ASN][1000 genomes]
rs17092497	0.89[AFR][1000 genomes]
rs17092542	0.88[AFR][1000 genomes]
rs17095662	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17586888	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17663387	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17663670	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1924034	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1966384	0.88[AFR][1000 genomes]
rs2016966	0.80[ASN][1000 genomes]
rs2146805	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146806	0.88[AFR][1000 genomes]
rs2181563	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2286632	0.80[ASN][1000 genomes]
rs2420066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420067	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420069	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3180654	0.89[AFR][1000 genomes]
rs34064819	0.89[AFR][1000 genomes]
rs34683721	0.89[AFR][1000 genomes]
rs35010779	0.88[AFR][1000 genomes]
rs35221086	0.86[ASN][1000 genomes]
rs35453961	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35622181	0.88[AFR][1000 genomes]
rs35628210	0.88[AFR][1000 genomes]
rs3758603	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41284358	0.89[AFR][1000 genomes]
rs4277024	0.81[ASN][1000 genomes]
rs4752255	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4752256	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4752322	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4752347	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55671354	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55759483	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58587374	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60820172	0.88[AFR][1000 genomes]
rs61596353	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61867965	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61868018	0.89[AFR][1000 genomes]
rs61868024	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6585300	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7072356	0.88[AFR][1000 genomes]
rs7072364	0.89[AFR][1000 genomes]
rs7074729	0.86[AFR][1000 genomes]
rs7075888	0.87[AFR][1000 genomes]
rs7077148	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7079877	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081975	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7082836	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7093674	0.84[AFR][1000 genomes]
rs7093686	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7094072	0.88[AFR][1000 genomes]
rs7095816	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72833128	0.81[ASN][1000 genomes]
rs72833130	0.81[ASN][1000 genomes]
rs758585	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs765173	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs765174	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7895551	0.88[AFR][1000 genomes]
rs7895830	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7897937	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7898347	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7903663	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7904188	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7907837	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7908237	0.89[EUR][1000 genomes]
rs7908665	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7909566	0.88[AFR][1000 genomes]
rs7909657	0.88[AFR][1000 genomes]
rs7914792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7915943	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7918129	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7918253	0.89[AFR][1000 genomes]
rs7918388	0.89[AFR][1000 genomes]
rs7919649	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7920216	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7923295	0.89[AFR][1000 genomes]
rs7923693	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8181444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	esv3338822	chr10:116579462-116583960	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2420065	FAM160B1	cis	Esophagus Muscularis	GTEx
rs2420065	FAM160B1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116580600-116583800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr10:116580600-116584600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr10:116580800-116584200	Active TSS	NHLF	lung
4	chr10:116580800-116584600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:116581000-116583800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr10:116581000-116583800	Active TSS	Right Atrium	heart
7	chr10:116581000-116584400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr10:116581000-116584800	Active TSS	Aorta	Aorta
9	chr10:116581200-116583800	Active TSS	Adipose Nuclei	Adipose
10	chr10:116582200-116585200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:116582600-116584200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
12	chr10:116582600-116584600	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr10:116582600-116585800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr10:116582600-116589000	Weak transcription	Gastric	stomach
15	chr10:116582600-116589400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr10:116582600-116596800	Weak transcription	Lung	lung
17	chr10:116582600-116597000	Weak transcription	Spleen	Spleen
18	chr10:116582800-116584000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr10:116582800-116584200	Enhancers	Primary B cells from peripheral blood	blood
20	chr10:116582800-116584600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr10:116582800-116584800	Weak transcription	Pancreas	Pancrea
22	chr10:116582800-116585800	Weak transcription	Left Ventricle	heart
23	chr10:116582800-116589000	Weak transcription	Right Ventricle	heart
24	chr10:116582800-116593000	Weak transcription	Colonic Mucosa	Colon
25	chr10:116582800-116604400	Weak transcription	Esophagus	oesophagus
26	chr10:116583000-116583800	Weak transcription	Brain Angular Gyrus	brain
27	chr10:116583000-116583800	Weak transcription	Brain Hippocampus Middle	brain
28	chr10:116583000-116583800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr10:116583000-116583800	Weak transcription	Stomach Mucosa	stomach
30	chr10:116583000-116584000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr10:116583000-116584000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr10:116583000-116584200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr10:116583000-116584400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr10:116583000-116584600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr10:116583000-116584800	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr10:116583000-116584800	Enhancers	Rectal Smooth Muscle	rectum
37	chr10:116583000-116585400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
38	chr10:116583000-116586000	Enhancers	Fetal Heart	heart
39	chr10:116583000-116586200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr10:116583000-116586800	Enhancers	Placenta	Placenta
41	chr10:116583000-116589400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr10:116583000-116593200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr10:116583000-116594800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:116583000-116596200	Weak transcription	Brain Substantia Nigra	brain
45	chr10:116583000-116617600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr10:116583200-116583800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr10:116583200-116583800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr10:116583200-116583800	Enhancers	Primary B cells from cord blood	blood
49	chr10:116583200-116583800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr10:116583200-116583800	Enhancers	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links