Variant report

Variant	rs2663038
Chromosome Location	chr10:50099468-50099469
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10745284	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10776650	0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs10776651	0.89[ASN][1000 genomes]
rs10776652	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10857650	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10857651	0.81[ASN][1000 genomes]
rs11101517	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11101533	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11101558	0.90[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs11595341	0.88[ASN][1000 genomes]
rs17836494	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1904595	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1904600	0.89[ASN][1000 genomes]
rs1904604	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1904605	0.89[ASN][1000 genomes]
rs1913517	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1993985	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2127586	0.89[ASN][1000 genomes]
rs2127592	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2170133	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2377653	0.94[ASN][1000 genomes]
rs2377654	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2620878	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2620880	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2620881	0.80[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2620882	0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2620883	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2620884	0.89[ASN][1000 genomes]
rs2620885	0.89[ASN][1000 genomes]
rs2620887	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2620890	0.84[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2620893	0.80[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2620894	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2620907	0.80[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2663019	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2663020	0.84[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs2663021	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2663029	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2663030	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2663033	0.89[ASN][1000 genomes]
rs2663034	0.90[ASN][1000 genomes]
rs2663041	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2663049	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2663050	0.89[ASN][1000 genomes]
rs2663052	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2663054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2663069	0.88[ASN][1000 genomes]
rs2671692	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.95[ASN][1000 genomes]
rs2671694	0.90[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs2671710	0.92[ASN][1000 genomes]
rs2671711	0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2671712	0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2889699	0.89[ASN][1000 genomes]
rs2928404	0.89[ASN][1000 genomes]
rs2940712	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2940728	0.90[ASN][1000 genomes]
rs2940729	0.89[ASN][1000 genomes]
rs2940730	0.94[ASN][1000 genomes]
rs2943245	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2943255	0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3747878	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3827683	0.81[ASN][1000 genomes]
rs3860191	0.90[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs4838657	0.88[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs6537581	0.84[ASN][1000 genomes]
rs6537582	0.84[ASN][1000 genomes]
rs6537583	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7068839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7069142	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7078312	0.84[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7086101	0.88[ASN][1000 genomes]
rs7086333	0.90[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs7088194	0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7094610	0.83[CHD][hapmap]
rs7094742	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7097397	0.82[JPT][hapmap]
rs7098906	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7900483	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7912174	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7913620	0.90[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs7915025	0.85[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7916558	0.89[ASN][1000 genomes]
rs7922169	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7923621	0.88[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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv831865	chr10:49994254-50164239	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2663038	PRKG1	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50072800-50126200	Strong transcription	Primary B cells from peripheral blood	blood
2	chr10:50074200-50107000	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr10:50074600-50129600	Strong transcription	Primary B cells from cord blood	blood
4	chr10:50075400-50126000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr10:50088000-50109400	Weak transcription	Right Atrium	heart
6	chr10:50092600-50106800	Weak transcription	Primary T cells from cord blood	blood
7	chr10:50096600-50103600	Strong transcription	GM12878-XiMat	blood
8	chr10:50096600-50106200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr10:50096600-50107800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr10:50097400-50100400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr10:50098000-50105400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr10:50098000-50110000	Strong transcription	Primary hematopoietic stem cells	blood
13	chr10:50098200-50110200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr10:50098800-50099800	Enhancers	Esophagus	oesophagus
15	chr10:50099000-50100600	Enhancers	Fetal Lung	lung
16	chr10:50099000-50102600	Weak transcription	Lung	lung
17	chr10:50099400-50099600	Enhancers	Adipose Nuclei	Adipose
18	chr10:50099400-50099800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr10:50099400-50100400	Enhancers	HSMMtube	muscle
20	chr10:50099400-50102600	Weak transcription	Spleen	Spleen

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