Variant report

Variant	rs10462539
Chromosome Location	chr5:75703047-75703048
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10043040	0.89[EUR][1000 genomes]
rs10044351	0.89[EUR][1000 genomes]
rs10044370	0.89[EUR][1000 genomes]
rs10044373	0.89[EUR][1000 genomes]
rs10065322	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10068074	0.89[EUR][1000 genomes]
rs10068404	0.82[EUR][1000 genomes]
rs10070688	0.89[EUR][1000 genomes]
rs10072221	0.89[EUR][1000 genomes]
rs10073228	0.89[EUR][1000 genomes]
rs10073282	0.89[EUR][1000 genomes]
rs10073382	0.91[EUR][1000 genomes]
rs10073448	0.91[EUR][1000 genomes]
rs10077372	0.89[EUR][1000 genomes]
rs10079393	0.88[EUR][1000 genomes]
rs10462540	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1122654	0.80[ASN][1000 genomes]
rs11738470	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11740038	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11744637	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11747990	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11749318	0.89[EUR][1000 genomes]
rs12523532	0.89[EUR][1000 genomes]
rs13175420	0.90[EUR][1000 genomes]
rs13357820	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1984636	0.80[ASN][1000 genomes]
rs28386181	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3886042	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3886043	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4254886	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4296785	0.85[ASN][1000 genomes]
rs4501323	0.85[ASN][1000 genomes]
rs4501324	0.85[ASN][1000 genomes]
rs4615280	0.89[EUR][1000 genomes]
rs4704310	0.85[ASN][1000 genomes]
rs55995866	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56189196	0.89[EUR][1000 genomes]
rs57929471	0.82[ASN][1000 genomes]
rs59428516	0.88[EUR][1000 genomes]
rs60570368	0.89[EUR][1000 genomes]
rs62363210	0.84[ASN][1000 genomes]
rs6453217	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6865628	0.90[EUR][1000 genomes]
rs6887962	0.90[EUR][1000 genomes]
rs6895725	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7706926	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7707426	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7718641	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7731240	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	nsv870415	chr5:75526088-75738412	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv882206	chr5:75676658-75746813	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75700000-75703400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr5:75700000-75703400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:75700000-75703600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr5:75700200-75704600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr5:75700600-75703200	Enhancers	Primary B cells from peripheral blood	blood
6	chr5:75700600-75707400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:75700800-75707200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr5:75701000-75703400	Enhancers	Primary T cells from cord blood	blood
9	chr5:75701000-75703400	Enhancers	K562	blood
10	chr5:75701000-75706200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:75701000-75721600	Weak transcription	Fetal Stomach	stomach
12	chr5:75701200-75704400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr5:75701200-75704400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr5:75701200-75706800	Enhancers	Primary T cells fromperipheralblood	blood
15	chr5:75701400-75705400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:75701600-75703800	Enhancers	Primary B cells from cord blood	blood
17	chr5:75701600-75707200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr5:75701600-75707200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr5:75701600-75713000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr5:75701800-75703200	Enhancers	Small Intestine	intestine
21	chr5:75701800-75704400	Enhancers	Stomach Mucosa	stomach
22	chr5:75701800-75705800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr5:75701800-75706600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr5:75701800-75707000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr5:75702000-75704800	Enhancers	Placenta	Placenta
26	chr5:75702000-75706400	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr5:75702000-75707800	Enhancers	HepG2	liver
28	chr5:75702200-75704400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr5:75702200-75705400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr5:75702200-75707800	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr5:75702400-75703800	Enhancers	Duodenum Mucosa	Duodenum
32	chr5:75702400-75705400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr5:75702600-75703200	Enhancers	GM12878-XiMat	blood
34	chr5:75702600-75703600	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr5:75702600-75704200	Weak transcription	Fetal Intestine Small	intestine
36	chr5:75702600-75704400	Enhancers	Liver	Liver
37	chr5:75702600-75706200	Enhancers	Primary hematopoietic stem cells	blood
38	chr5:75702600-75707200	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr5:75702800-75703200	Enhancers	Adipose Nuclei	Adipose
40	chr5:75702800-75703200	Enhancers	Gastric	stomach
41	chr5:75702800-75703400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr5:75702800-75704400	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr5:75702800-75704400	Enhancers	Pancreas	Pancrea
44	chr5:75703000-75703400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr5:75703000-75731800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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