Variant report

Variant	rs11161695
Chromosome Location	chr1:86339672-86339673
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 97 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1072508	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs1072509	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs10782561	0.81[EUR][1000 genomes]
rs10873730	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10873731	0.86[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1112327	0.95[CEU][hapmap]
rs11161693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11161696	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs11161697	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs12029238	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12124109	0.93[ASN][1000 genomes]
rs12127479	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1564516	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs167518	0.91[ASN][1000 genomes]
rs1698733	0.89[CEU][hapmap];0.86[TSI][hapmap]
rs172693	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs172694	0.90[ASN][1000 genomes]
rs17411495	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs186376	0.91[CHB][hapmap]
rs188763	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1904947	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2256515	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2795038	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2892901	0.81[ASN][1000 genomes]
rs313701	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs313702	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs313703	0.95[CHB][hapmap]
rs313704	0.91[CHB][hapmap]
rs313705	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs313706	0.91[CHB][hapmap]
rs313707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs313708	0.95[CHB][hapmap]
rs313709	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs313738	0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs313739	0.91[ASN][1000 genomes]
rs313740	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs313741	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs313742	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs313743	0.89[ASN][1000 genomes]
rs313744	0.89[ASN][1000 genomes]
rs313745	0.90[ASN][1000 genomes]
rs313746	0.86[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.91[ASN][1000 genomes]
rs313749	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs313754	0.82[ASN][1000 genomes]
rs313756	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs313757	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs313758	0.86[CHB][hapmap]
rs313759	0.86[CHB][hapmap]
rs313760	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs313761	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs313762	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs313763	0.95[CHB][hapmap]
rs313764	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs313765	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs313766	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs313767	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs313768	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs313769	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs313770	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs313771	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs313772	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs313774	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs313775	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs383588	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs428475	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs437257	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs445782	0.93[ASN][1000 genomes]
rs4486475	0.96[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs482789	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs486726	0.96[CEU][hapmap]
rs537408	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs556247	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs559247	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs573444	0.85[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs578615	0.96[CEU][hapmap]
rs593146	0.85[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap]
rs603297	0.96[CEU][hapmap]
rs605060	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs61785081	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61785083	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6576793	0.91[CHB][hapmap]
rs6673508	0.96[CEU][hapmap]
rs6701281	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs693436	0.85[CEU][hapmap];0.81[CHB][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap]
rs7512039	0.87[CEU][hapmap]
rs7524286	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7526013	0.84[CEU][hapmap]
rs7536101	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7544141	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7549218	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs861933	0.96[CEU][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv546721	chr1:86226352-86392577	Weak transcription Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv999743	chr1:86241246-86364846	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1011293	chr1:86270649-86416972	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	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
6	nsv871189	chr1:86315724-86402244	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11161695	LOC339524	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86331400-86341600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr1:86331800-86339800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:86333200-86343800	Weak transcription	GM12878-XiMat	blood
4	chr1:86339200-86339800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
5	chr1:86339200-86341200	Strong transcription	Fetal Lung	lung
6	chr1:86339400-86342600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:86339600-86342400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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