Variant report

Variant	rs425858
Chromosome Location	chr1:179234478-179234479
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1046385	0.94[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs1078872	0.85[GIH][hapmap]
rs10798670	0.81[CHB][hapmap]
rs10913690	0.80[GIH][hapmap]
rs10913691	0.84[EUR][1000 genomes]
rs10913697	0.85[GIH][hapmap]
rs10913733	0.81[CHB][hapmap]
rs1173077	0.93[GIH][hapmap];0.81[JPT][hapmap]
rs12022539	0.94[CEU][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs12026030	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12028643	0.87[EUR][1000 genomes]
rs12031894	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12035050	0.85[EUR][1000 genomes]
rs12045521	0.85[EUR][1000 genomes]
rs12049122	0.85[EUR][1000 genomes]
rs12049237	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs12073970	0.86[CHB][hapmap]
rs12097041	0.81[CHB][hapmap]
rs12120123	0.81[CHB][hapmap]
rs12130276	0.85[GIH][hapmap]
rs12130876	0.81[CHB][hapmap]
rs12138436	0.81[CHB][hapmap]
rs12402165	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs12404921	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12405133	0.81[CHB][hapmap]
rs12405321	0.81[CHB][hapmap]
rs12408349	0.94[CEU][hapmap];0.81[CHB][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12408668	0.84[EUR][1000 genomes]
rs12725126	0.81[CHB][hapmap]
rs12740455	0.81[CHB][hapmap]
rs12745772	0.81[CHB][hapmap]
rs12759446	0.84[CHB][hapmap]
rs1325194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs13306731	0.81[CHB][hapmap]
rs13374852	0.81[CHB][hapmap]
rs1475798	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs16853917	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs16853936	0.94[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs17362081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs1856968	0.85[GIH][hapmap]
rs2050922	0.84[EUR][1000 genomes]
rs2066162	0.88[EUR][1000 genomes]
rs2068234	0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs2130576	0.85[GIH][hapmap]
rs2152317	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs2171959	0.85[GIH][hapmap]
rs2493124	0.85[GIH][hapmap]
rs2636266	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2636274	0.85[GIH][hapmap]
rs2636276	0.80[GIH][hapmap]
rs2636278	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs2636280	0.85[GIH][hapmap]
rs2636287	0.84[JPT][hapmap]
rs2636289	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2636290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs2791941	0.80[GIH][hapmap]
rs2793791	0.85[EUR][1000 genomes]
rs2793796	0.85[GIH][hapmap]
rs2793797	0.85[GIH][hapmap]
rs2793799	0.93[GIH][hapmap];0.81[JPT][hapmap]
rs2793804	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2793807	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2793808	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2793812	0.83[GIH][hapmap]
rs2793816	0.90[GIH][hapmap];0.81[TSI][hapmap]
rs2816179	0.94[EUR][1000 genomes]
rs2816180	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2816203	0.85[GIH][hapmap]
rs2816209	0.90[GIH][hapmap];0.81[JPT][hapmap]
rs2816213	0.85[GIH][hapmap]
rs3122378	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3210839	0.85[GIH][hapmap];0.81[JPT][hapmap]
rs3753524	0.94[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs380951	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3813642	0.80[GIH][hapmap]
rs3813643	0.80[GIH][hapmap]
rs3818433	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs4077551	0.81[CHB][hapmap]
rs4077552	0.81[CHB][hapmap]
rs410589	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4133136	0.80[CHB][hapmap]
rs413881	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4478776	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs451088	0.88[GIH][hapmap]
rs4651014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs58284152	0.84[EUR][1000 genomes]
rs58948941	0.82[EUR][1000 genomes]
rs59777301	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60595009	0.84[EUR][1000 genomes]
rs61821690	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61821735	0.89[EUR][1000 genomes]
rs61821737	0.85[EUR][1000 genomes]
rs61821738	0.86[EUR][1000 genomes]
rs61821739	0.86[EUR][1000 genomes]
rs61821740	0.86[EUR][1000 genomes]
rs61824363	0.86[EUR][1000 genomes]
rs61824364	0.86[EUR][1000 genomes]
rs61824365	0.85[EUR][1000 genomes]
rs61824368	0.83[EUR][1000 genomes]
rs61824371	0.85[EUR][1000 genomes]
rs61824388	0.85[EUR][1000 genomes]
rs61824389	0.85[EUR][1000 genomes]
rs6675772	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6694339	0.81[EUR][1000 genomes]
rs7414502	0.86[EUR][1000 genomes]
rs915337	0.88[GIH][hapmap]
rs931441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9728480	0.85[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs425858	IER5	cis	cerebellum	SCAN
rs425858	LHX4	cis	parietal	SCAN
rs425858	FAM20B	cis	parietal	SCAN
rs425858	ABL2	cis	parietal	SCAN
rs425858	ABL2	cis	cerebellum	SCAN
rs425858	TOR3A	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179232200-179241800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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