Variant report

Variant	rs313746
Chromosome Location	chr1:86278315-86278316
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86278102..86279954-chr1:86282044..86284732,2	K562	blood:

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1072508	0.91[CHB][hapmap]
rs1072509	0.91[CHB][hapmap]
rs10873730	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10873731	1.00[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[ASN][1000 genomes]
rs11161693	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11161695	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]
rs11161696	0.91[CHB][hapmap];0.80[CHD][hapmap]
rs11161697	0.91[CHB][hapmap]
rs12029238	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12124109	0.91[ASN][1000 genomes]
rs12127479	0.91[ASN][1000 genomes]
rs1564516	0.95[CHB][hapmap]
rs167518	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs172693	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs172694	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17411495	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs186376	0.86[CHB][hapmap]
rs188763	0.89[ASN][1000 genomes]
rs1904947	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2256515	0.91[ASN][1000 genomes]
rs2795038	0.91[ASN][1000 genomes]
rs313701	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs313702	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs313703	0.90[CHB][hapmap]
rs313704	0.86[CHB][hapmap]
rs313705	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs313706	0.86[CHB][hapmap]
rs313707	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs313708	0.91[CHB][hapmap];0.80[CHD][hapmap]
rs313709	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs313710	0.81[MKK][hapmap];0.84[TSI][hapmap]
rs313732	0.82[CEU][hapmap]
rs313734	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs313738	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs313739	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313742	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313743	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs313744	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs313745	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs313749	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs313754	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs313755	0.81[AMR][1000 genomes]
rs313756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs313757	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs313758	0.91[CHB][hapmap]
rs313759	0.91[CHB][hapmap]
rs313760	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs313761	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs313762	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs313763	0.90[CHB][hapmap]
rs313764	0.91[ASN][1000 genomes]
rs313765	0.84[ASN][1000 genomes]
rs313766	0.91[ASN][1000 genomes]
rs313767	0.87[ASN][1000 genomes]
rs313768	0.91[ASN][1000 genomes]
rs313769	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs313770	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs313771	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs313772	0.84[ASN][1000 genomes]
rs313774	0.89[ASN][1000 genomes]
rs313775	0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs366187	0.81[CEU][hapmap];0.87[TSI][hapmap]
rs380654	0.81[CEU][hapmap]
rs383588	0.94[ASN][1000 genomes]
rs428475	0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs437257	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs445782	0.91[ASN][1000 genomes]
rs482789	0.91[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs537408	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs556247	0.91[ASN][1000 genomes]
rs573444	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs593146	0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap]
rs598104	0.84[CEU][hapmap]
rs61785081	0.91[ASN][1000 genomes]
rs61785083	0.90[ASN][1000 genomes]
rs6576793	0.86[CHB][hapmap]
rs693436	0.82[JPT][hapmap]
rs7524286	0.95[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs7536101	0.95[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs7544141	0.91[ASN][1000 genomes]
rs7549218	0.82[ASN][1000 genomes]

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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs313746	LOC339524	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86275200-86282000	Weak transcription	Fetal Lung	lung
2	chr1:86276000-86278600	Strong transcription	Primary hematopoietic stem cells	blood
3	chr1:86276400-86280200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr1:86276400-86284200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:86277000-86279000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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