Variant report

Variant	rs66609380
Chromosome Location	chr3:23940077-23940078
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:23935883..23937649-chr3:23937998..23940672,2	K562	blood:
2	chr3:23938348..23940828-chr3:23949135..23950693,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10084748	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1037635	1.00[ASN][1000 genomes]
rs11129128	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070128	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13087250	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13316457	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317815	0.87[EUR][1000 genomes]
rs13321439	0.87[EUR][1000 genomes]
rs13321440	0.87[EUR][1000 genomes]
rs1533141	0.85[EUR][1000 genomes]
rs1567579	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567580	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28524116	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34036067	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34058540	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34082882	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34593533	0.87[EUR][1000 genomes]
rs34866549	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953164	1.00[ASN][1000 genomes]
rs35136361	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35457462	0.94[EUR][1000 genomes]
rs35755171	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35755253	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36063721	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36089963	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762775	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935253	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4131404	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4300960	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490300	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535169	1.00[ASN][1000 genomes]
rs4602333	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858096	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4858554	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4858556	1.00[ASN][1000 genomes]
rs4858564	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932805	1.00[ASN][1000 genomes]
rs6550808	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67002637	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67236598	1.00[ASN][1000 genomes]
rs67606949	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767005	1.00[ASN][1000 genomes]
rs6770052	0.87[EUR][1000 genomes]
rs6775878	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6776201	1.00[ASN][1000 genomes]
rs6776568	1.00[ASN][1000 genomes]
rs6778577	0.85[EUR][1000 genomes]
rs6790140	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791805	1.00[ASN][1000 genomes]
rs6803214	1.00[ASN][1000 genomes]
rs6803587	0.87[EUR][1000 genomes]
rs71324126	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150266	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73150299	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610689	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7610935	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7611018	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs954748	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9809225	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812419	1.00[ASN][1000 genomes]
rs9812870	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9817923	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9853954	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855481	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859567	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9863176	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875577	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882067	1.00[ASN][1000 genomes]
rs9883834	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23901200-23942000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:23907600-23940200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:23908000-23940200	Weak transcription	Gastric	stomach
4	chr3:23916000-23950200	Weak transcription	Aorta	Aorta
5	chr3:23916200-23948800	Weak transcription	Colonic Mucosa	Colon
6	chr3:23919200-23940200	Weak transcription	Pancreas	Pancrea
7	chr3:23920800-23940200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:23922400-23956600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:23923000-23956600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:23923400-23955200	Weak transcription	Thymus	Thymus
11	chr3:23923400-23957000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:23923600-23956800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:23924200-23957800	Weak transcription	Esophagus	oesophagus
14	chr3:23924200-23957800	Weak transcription	Lung	lung
15	chr3:23924400-23940200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:23924600-23940200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr3:23925000-23940200	Weak transcription	Fetal Brain Female	brain
18	chr3:23928000-23957200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr3:23928800-23956000	Weak transcription	Small Intestine	intestine
20	chr3:23928800-23957400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:23929000-23956600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:23929800-23944200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:23930600-23945800	Weak transcription	Fetal Heart	heart
24	chr3:23930800-23954800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:23930800-23956800	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:23931200-23945800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr3:23931600-23942600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:23931800-23940200	Weak transcription	Left Ventricle	heart
29	chr3:23931800-23940200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:23932000-23940200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr3:23932000-23955400	Weak transcription	NHEK	skin
32	chr3:23932200-23940200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:23933200-23940400	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:23934000-23944000	Weak transcription	HSMMtube	muscle
35	chr3:23934200-23956600	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr3:23934400-23956400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:23934600-23940200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr3:23934600-23940200	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:23934600-23942200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:23934600-23945800	Weak transcription	Hela-S3	cervix
41	chr3:23934600-23947600	Strong transcription	Fetal Stomach	stomach
42	chr3:23934800-23940200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr3:23934800-23940200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:23934800-23940200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:23935000-23940200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:23935000-23940600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:23935000-23957400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:23935800-23954400	Weak transcription	NH-A	brain
49	chr3:23935800-23954600	Weak transcription	HUVEC	blood vessel
50	chr3:23936000-23940200	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links