Variant report

Variant	rs1904596
Chromosome Location	chr10:50080311-50080312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10776647	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10776648	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10857655	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11101511	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs11101529	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11101530	0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11101531	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11101532	0.90[ASN][1000 genomes]
rs2002587	0.90[ASN][1000 genomes]
rs2002588	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2127590	0.89[JPT][hapmap]
rs2170132	0.89[JPT][hapmap]
rs2250389	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2448540	0.89[JPT][hapmap]
rs2448545	0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2457214	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2620891	0.81[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2620896	0.85[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2620898	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2620904	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2663041	0.82[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2663044	0.89[JPT][hapmap]
rs2663051	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2663055	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2671694	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs2671695	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2928401	0.89[JPT][hapmap]
rs2940710	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2940727	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2943244	0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2943245	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs35932562	0.90[ASN][1000 genomes]
rs3747872	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3747873	0.90[ASN][1000 genomes]
rs3747874	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3747875	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3747877	0.90[ASN][1000 genomes]
rs3860188	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3860189	0.89[ASN][1000 genomes]
rs3860190	0.90[ASN][1000 genomes]
rs6537576	0.89[JPT][hapmap]
rs6537580	0.92[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs7079766	0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7093474	0.90[ASN][1000 genomes]
rs726786	0.89[JPT][hapmap]
rs7900138	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs7913005	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7919656	0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs877819	0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs877820	0.90[ASN][1000 genomes]
rs877821	0.89[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
rs1904596	AL359058	trans	multi-tissue	Pritchard

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50054400-50081600	Weak transcription	Spleen	Spleen
2	chr10:50072200-50087800	Weak transcription	Gastric	stomach
3	chr10:50072800-50126200	Strong transcription	Primary B cells from peripheral blood	blood
4	chr10:50074200-50107000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr10:50074600-50093200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr10:50074600-50129600	Strong transcription	Primary B cells from cord blood	blood
7	chr10:50075200-50093600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr10:50075400-50126000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr10:50076600-50092000	Weak transcription	Primary T cells from cord blood	blood
10	chr10:50077800-50081200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr10:50079000-50081800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr10:50079400-50081400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr10:50079400-50088400	Strong transcription	GM12878-XiMat	blood
14	chr10:50080200-50088400	Strong transcription	Primary hematopoietic stem cells	blood

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