Variant report

Variant	rs2620888
Chromosome Location	chr10:49978113-49978114
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10776643	0.86[EUR][1000 genomes]
rs11101469	0.87[EUR][1000 genomes]
rs11101470	0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs11101471	0.85[EUR][1000 genomes]
rs11101511	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs11595065	0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs11598212	0.86[EUR][1000 genomes]
rs2127590	0.93[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs2170132	0.93[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs2448539	0.86[CHB][hapmap]
rs2448540	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs2457214	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2620889	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2620896	0.89[JPT][hapmap]
rs2663043	1.00[LWK][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2663044	0.89[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2663053	0.89[ASN][1000 genomes]
rs2683610	1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2928393	0.87[ASN][1000 genomes]
rs2928401	0.89[JPT][hapmap]
rs4838648	0.84[ASN][1000 genomes]
rs6537576	1.00[CEU][hapmap];0.93[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs726786	0.93[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap]
rs7904251	0.84[TSI][hapmap];0.86[EUR][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	nsv895374	chr10:49969556-49990081	Strong transcription Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2620888	PRKG1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49962400-49980600	Strong transcription	Primary B cells from cord blood	blood
2	chr10:49967600-50000000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr10:49967800-49978200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr10:49967800-49979000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr10:49967800-50006800	Strong transcription	Primary B cells from peripheral blood	blood
6	chr10:49968600-49978600	Weak transcription	Adipose Nuclei	Adipose
7	chr10:49969400-49989800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr10:49971400-49982600	Weak transcription	Spleen	Spleen
9	chr10:49975200-49982400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr10:49976400-49981200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr10:49976800-49980000	Strong transcription	GM12878-XiMat	blood
12	chr10:49977000-49979000	Weak transcription	Fetal Stomach	stomach
13	chr10:49977000-49990400	Weak transcription	Fetal Brain Male	brain
14	chr10:49977200-49978200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr10:49977200-49978200	Strong transcription	Primary hematopoietic stem cells	blood
16	chr10:49977200-49978400	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr10:49977400-49979400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr10:49977400-49981200	Weak transcription	Fetal Thymus	thymus
19	chr10:49977800-49978200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr10:49977800-49979600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:49977800-49980200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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