Variant report

Variant	rs1562422
Chromosome Location	chr6:25044577-25044578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12524842	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525328	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12525405	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12528227	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661796	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12663160	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13195161	0.95[ASN][1000 genomes]
rs13196712	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203073	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13218879	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447243	0.80[ASN][1000 genomes]
rs1562423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1597011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1597012	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs160034	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1900551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923192	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1923193	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs192773	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2273671	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs302992	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs303879	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs303880	0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs303884	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34322558	0.84[EUR][1000 genomes]
rs34475409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34693126	0.90[ASN][1000 genomes]
rs35028017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35553146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36030790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3792974	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs3792983	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs4711071	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711072	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4711073	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4712882	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56108659	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66577954	0.80[ASN][1000 genomes]
rs67240854	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67795839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738141	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs895676	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9348660	0.80[ASN][1000 genomes]
rs9358827	0.94[JPT][hapmap]
rs9461093	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1562422	PSG2	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25035200-25044600	Weak transcription	Right Atrium	heart
2	chr6:25042200-25050200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:25043000-25044600	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr6:25043000-25044600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr6:25043000-25044800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:25043000-25044800	Enhancers	Placenta	Placenta
7	chr6:25043200-25044800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr6:25043200-25053400	Weak transcription	Spleen	Spleen
9	chr6:25043400-25044600	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr6:25043400-25050800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr6:25043800-25050200	Weak transcription	Primary B cells from cord blood	blood
12	chr6:25044000-25044800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr6:25044000-25045000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr6:25044200-25044600	Enhancers	GM12878-XiMat	blood
15	chr6:25044200-25047200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr6:25044200-25050000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:25044400-25044600	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr6:25044400-25049600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:25044400-25049600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:25044400-25049800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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