Variant report

Variant	rs62308155
Chromosome Location	chr4:57812132-57812133
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POLR2B-7	chr4:57811722-57812681	NONHSAT096529

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10030913	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10866440	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10866441	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1105434	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1107675	0.82[ASN][1000 genomes]
rs11729152	0.85[ASN][1000 genomes]
rs11730525	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11734953	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11736808	0.81[ASN][1000 genomes]
rs11736869	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11736965	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11737689	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11932673	0.83[ASN][1000 genomes]
rs11933908	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12500454	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12501224	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12501990	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12502076	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13108245	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13113802	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13116564	0.83[ASN][1000 genomes]
rs13119525	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13123018	0.87[EUR][1000 genomes]
rs13131605	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13136432	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13146539	0.85[ASN][1000 genomes]
rs13146960	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13149162	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13150593	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13152476	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13353552	0.82[ASN][1000 genomes]
rs17087307	0.83[ASN][1000 genomes]
rs17087317	0.83[ASN][1000 genomes]
rs1718839	0.80[ASN][1000 genomes]
rs1877669	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1963666	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1976780	0.83[ASN][1000 genomes]
rs2014870	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2090962	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2228991	0.85[ASN][1000 genomes]
rs2412772	0.90[EUR][1000 genomes]
rs3000	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34124552	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34448457	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34659774	0.83[ASN][1000 genomes]
rs35267092	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3796528	0.85[ASN][1000 genomes]
rs4276341	0.83[ASN][1000 genomes]
rs4864606	0.86[ASN][1000 genomes]
rs4864607	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4864608	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55822707	0.86[ASN][1000 genomes]
rs62308135	0.86[ASN][1000 genomes]
rs62308136	0.86[ASN][1000 genomes]
rs62308137	0.85[ASN][1000 genomes]
rs6554397	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6554398	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6554399	0.85[ASN][1000 genomes]
rs6838948	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6852110	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6854420	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6855212	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs729844	0.83[ASN][1000 genomes]
rs73242609	0.86[ASN][1000 genomes]
rs73242616	0.83[ASN][1000 genomes]
rs7666804	0.83[ASN][1000 genomes]
rs7667302	0.83[ASN][1000 genomes]
rs7680734	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7685576	0.83[ASN][1000 genomes]
rs7695970	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs781665	0.80[ASN][1000 genomes]
rs781666	0.80[ASN][1000 genomes]
rs781668	0.80[ASN][1000 genomes]
rs781669	0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs899632	0.83[ASN][1000 genomes]
rs9684742	0.83[ASN][1000 genomes]
rs9942208	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	esv3425352	chr4:57783591-57820951	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62308155	RP11-738E22.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57793600-57842000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:57793600-57842000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:57798000-57814200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr4:57798200-57828400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:57798200-57829600	Weak transcription	Pancreas	Pancrea
6	chr4:57798400-57814000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:57798400-57828200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr4:57798600-57828200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr4:57803800-57828400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr4:57804200-57824200	Weak transcription	NH-A	brain
11	chr4:57804800-57812400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:57804800-57826600	Weak transcription	Liver	Liver
13	chr4:57805000-57830800	Weak transcription	Colonic Mucosa	Colon
14	chr4:57805200-57812200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr4:57805400-57826400	Weak transcription	Primary T cells from cord blood	blood
16	chr4:57805600-57814200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:57805600-57826600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:57805800-57827400	Weak transcription	Placenta	Placenta
19	chr4:57806000-57814000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:57806000-57814800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr4:57806000-57827000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:57806000-57827200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:57806000-57827200	Weak transcription	Thymus	Thymus
24	chr4:57806200-57813600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr4:57806200-57826600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:57806200-57827400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:57808200-57827200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:57808600-57827000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:57811600-57812400	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links