Variant report

Variant	rs12564699
Chromosome Location	chr1:173678039-173678040
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 85 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10798290	0.90[CHB][hapmap]
rs10912651	0.84[CHB][hapmap]
rs10912670	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912671	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12039524	0.85[CHB][hapmap]
rs12082131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12086229	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12561931	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12565915	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12566945	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1322774	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs16846439	0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs1951625	0.95[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.90[TSI][hapmap];0.90[ASN][1000 genomes]
rs2067079	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2144708	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2208850	0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.90[ASN][1000 genomes]
rs2227612	0.90[CHB][hapmap]
rs2273366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2281486	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.90[ASN][1000 genomes]
rs2295366	0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.90[ASN][1000 genomes]
rs28804123	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3791020	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.89[ASN][1000 genomes]
rs45467799	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4558043	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4652283	0.90[CHB][hapmap]
rs4652298	0.90[CHB][hapmap]
rs4652328	0.90[CHB][hapmap]
rs55633896	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55829688	0.90[ASN][1000 genomes]
rs56019876	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56048122	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56138893	0.95[ASN][1000 genomes]
rs56369162	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56928371	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57799150	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58287165	0.94[ASN][1000 genomes]
rs58825445	0.88[ASN][1000 genomes]
rs59858609	0.94[ASN][1000 genomes]
rs60264384	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826805	0.95[ASN][1000 genomes]
rs61826806	0.95[ASN][1000 genomes]
rs61826809	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61826810	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61826812	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61826813	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61826821	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826856	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61826857	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61827860	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61827861	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61827863	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827865	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61827867	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827870	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827876	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61827877	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61827881	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61827925	0.90[ASN][1000 genomes]
rs6413827	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425251	0.90[CHB][hapmap]
rs6425253	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6425258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6425261	0.90[ASN][1000 genomes]
rs6668702	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673175	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674381	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6681766	0.91[ASW][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6691001	0.89[ASN][1000 genomes]
rs6696680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7514556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7515721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7521884	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7530546	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7541082	0.90[CHB][hapmap]
rs7546048	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7548171	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7552741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425416	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425431	0.90[CHB][hapmap]
rs9425433	0.90[CHB][hapmap]
rs9425745	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9425756	0.95[CHB][hapmap];0.91[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.88[ASN][1000 genomes]
rs9660881	0.90[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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv1014827	chr1:173653453-173692470	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription 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	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12564699	DARS2	cis	parietal	SCAN
rs12564699	DARS2	cis	cerebellum	SCAN
rs12564699	TNN	cis	parietal	SCAN
rs12564699	SLC9A11	cis	parietal	SCAN
rs12564699	RFWD2	cis	cerebellum	SCAN
rs12564699	PRDX6	cis	parietal	SCAN
rs12564699	DARS2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173678000-173678600	Enhancers	K562	blood

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