Variant report

Variant	rs2222712
Chromosome Location	chr2:178511430-178511431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:178507100..178511896-chr2:178515301..178517578,4	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10201367	0.84[EUR][1000 genomes]
rs10201883	0.84[EUR][1000 genomes]
rs10497497	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10497499	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11679730	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680632	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs12468046	1.00[CHD][hapmap]
rs12618150	1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12620285	1.00[CHB][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12621156	1.00[CHD][hapmap]
rs12988366	0.89[MEX][hapmap]
rs13017234	1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13017429	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025391	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025904	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13026012	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028757	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1317945	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13431105	1.00[CHB][hapmap]
rs1348851	0.88[MEX][hapmap]
rs1358326	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1358327	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446839	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs1527403	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534305	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1544001	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17326999	1.00[CHD][hapmap]
rs1918345	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1918346	0.85[EUR][1000 genomes]
rs1918347	0.90[EUR][1000 genomes]
rs1997206	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2091442	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178017	1.00[CHD][hapmap]
rs2365620	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2365621	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2695315	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap]
rs4110134	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4341975	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893827	1.00[CHD][hapmap]
rs4893967	0.87[EUR][1000 genomes]
rs4893970	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893973	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4893978	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4893979	0.87[EUR][1000 genomes]
rs5025340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433672	1.00[CHD][hapmap]
rs6433685	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433686	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433687	0.80[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433688	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721360	1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6723031	1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6723063	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6746233	0.91[EUR][1000 genomes]
rs6755382	0.89[EUR][1000 genomes]
rs6756918	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7560080	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560514	1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560737	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573345	1.00[CHB][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7577552	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578901	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586934	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7593753	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[AFR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7597640	0.80[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941271	1.00[CHB][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv583688	chr2:178427640-178540293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2222712	PRKRA	cis	parietal	SCAN
rs2222712	AGPS	cis	cerebellum	SCAN
rs2222712	OSBPL6	cis	parietal	SCAN
rs2222712	TTC30B	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178509000-178516600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:178510800-178511800	Enhancers	K562	blood
3	chr2:178511400-178512000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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