Variant report

Variant	rs593146
Chromosome Location	chr1:86439443-86439444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1072508	0.85[CHB][hapmap]
rs1072509	0.85[CHB][hapmap]
rs10873730	0.87[CEU][hapmap];0.84[CHB][hapmap]
rs10873731	0.96[MEX][hapmap];0.82[TSI][hapmap]
rs1112327	0.82[CEU][hapmap]
rs11161693	0.84[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs11161695	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs11161696	0.85[CHB][hapmap]
rs11161697	0.85[CHB][hapmap]
rs12029238	0.84[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1564516	0.90[CHB][hapmap]
rs17411495	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs186376	0.80[CHB][hapmap]
rs1904947	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs313701	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs313702	0.90[CHB][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap]
rs313703	0.85[CHB][hapmap]
rs313704	0.80[CHB][hapmap]
rs313705	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs313706	0.80[CHB][hapmap]
rs313707	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs313708	0.85[CHB][hapmap]
rs313709	0.81[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap]
rs313738	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs313740	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs313741	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs313742	0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs313746	0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs313756	0.86[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs313757	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs313763	0.85[CHB][hapmap]
rs313769	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs313770	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs313771	0.88[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap]
rs313775	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs428475	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs437257	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4486475	0.81[CEU][hapmap]
rs481277	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs482789	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs486726	0.81[CEU][hapmap]
rs522075	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs537408	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs559247	0.81[CEU][hapmap]
rs570288	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs573444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs578615	0.81[CEU][hapmap]
rs603297	0.81[CEU][hapmap]
rs605060	0.81[CEU][hapmap]
rs6576793	0.85[CHB][hapmap]
rs681639	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs693436	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524286	0.90[CHB][hapmap]
rs7536101	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap]
rs861933	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv462395	chr1:86379514-86457334	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv546726	chr1:86379514-86457334	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv462406	chr1:86412177-86509996	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv546757	chr1:86412177-86509996	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv546758	chr1:86438327-86483632	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs593146	LOC339524	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86421400-86441400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:86422800-86442400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:86425800-86441200	Weak transcription	Fetal Lung	lung
4	chr1:86434200-86440800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:86438200-86441000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:86438800-86441400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:86438800-86441600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:86439000-86440800	Weak transcription	GM12878-XiMat	blood

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