Variant report

Variant	rs4893987
Chromosome Location	chr2:178585514-178585515
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	chr2:178577863..178580571-chr2:178582573..178585584,3	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1004541	0.82[CHB][hapmap]
rs10175364	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10192481	0.82[CHB][hapmap]
rs10201180	0.82[CHB][hapmap]
rs10497488	1.00[JPT][hapmap]
rs10497489	1.00[JPT][hapmap]
rs10930805	0.82[CHB][hapmap]
rs11684634	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs12622125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13428806	1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1344916	0.92[ASN][1000 genomes]
rs1344917	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs1344925	1.00[JPT][hapmap]
rs1347731	0.82[CHB][hapmap]
rs1370655	1.00[JPT][hapmap]
rs1370662	0.82[CHB][hapmap]
rs1370663	0.82[CHB][hapmap]
rs1370664	0.82[CHB][hapmap]
rs1438037	0.92[ASN][1000 genomes]
rs1438038	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs1438039	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1438048	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1469973	0.82[CHB][hapmap]
rs1561319	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1561320	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs16865726	0.92[ASN][1000 genomes]
rs16865764	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs16865769	1.00[JPT][hapmap]
rs16865791	0.85[JPT][hapmap]
rs17400505	0.83[MEX][hapmap]
rs1866208	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1866209	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1866210	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs1866211	0.92[ASN][1000 genomes]
rs1866212	0.92[ASN][1000 genomes]
rs1898586	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1946812	0.85[JPT][hapmap]
rs1975321	0.82[CHB][hapmap]
rs1975324	0.92[ASN][1000 genomes]
rs2164857	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs2365889	0.92[ASN][1000 genomes]
rs28700947	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2886498	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs3754991	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3754993	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs3754994	0.92[ASN][1000 genomes]
rs3770023	0.82[CHB][hapmap]
rs3770028	1.00[JPT][hapmap]
rs3770034	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs3770042	0.92[ASN][1000 genomes]
rs3770043	1.00[JPT][hapmap]
rs3770047	0.85[JPT][hapmap]
rs3821007	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3821009	0.85[JPT][hapmap]
rs4893839	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs4893840	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs4893980	0.82[CHB][hapmap]
rs4893981	0.82[CHB][hapmap]
rs4893984	0.82[CHB][hapmap]
rs4893985	0.82[CHB][hapmap]
rs56362604	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57242051	0.90[ASN][1000 genomes]
rs61334857	0.90[ASN][1000 genomes]
rs6433693	0.92[ASN][1000 genomes]
rs6704720	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6718702	0.82[CHB][hapmap]
rs6756240	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs749207	1.00[CHB][hapmap];0.92[ASN][1000 genomes]
rs749208	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs7562835	1.00[JPT][hapmap]
rs7567851	0.85[JPT][hapmap]
rs7596360	0.82[CHB][hapmap]
rs934798	1.00[JPT][hapmap]
rs934809	0.82[CHB][hapmap]
rs998059	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs998060	0.92[ASN][1000 genomes]
rs998061	0.92[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	nsv1005854	chr2:178546907-178586608	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4893987	SP3	cis	parietal	SCAN
rs4893987	TTC30A	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178581000-178587800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:178584000-178589000	Weak transcription	Colon Smooth Muscle	Colon

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