Variant report

Variant	rs1418843
Chromosome Location	chr1:158450382-158450383
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 149 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs1002599	0.90[CHB][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap]
rs1032352	0.95[ASN][1000 genomes]
rs10489833	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs10489834	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap]
rs10489835	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs10797010	1.00[ASN][1000 genomes]
rs10797011	0.97[ASN][1000 genomes]
rs10797012	0.97[ASN][1000 genomes]
rs10797013	0.97[ASN][1000 genomes]
rs10797017	0.96[CEU][hapmap];0.80[YRI][hapmap]
rs10797020	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs10797022	0.95[ASN][1000 genomes]
rs10797023	0.95[ASN][1000 genomes]
rs10797024	0.95[ASN][1000 genomes]
rs10908651	1.00[ASN][1000 genomes]
rs10908652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908653	1.00[ASN][1000 genomes]
rs10908654	0.99[ASN][1000 genomes]
rs10908655	0.99[ASN][1000 genomes]
rs10908656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10908657	0.97[ASN][1000 genomes]
rs10908658	0.97[ASN][1000 genomes]
rs10908659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10908660	0.97[ASN][1000 genomes]
rs10908661	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs10908663	0.95[ASN][1000 genomes]
rs10908664	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908680	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1112915	1.00[ASN][1000 genomes]
rs11264976	0.98[ASN][1000 genomes]
rs11264977	0.99[ASN][1000 genomes]
rs11264978	1.00[ASN][1000 genomes]
rs11264981	1.00[ASN][1000 genomes]
rs11264983	0.99[ASN][1000 genomes]
rs11264984	0.97[ASN][1000 genomes]
rs11264985	0.97[ASN][1000 genomes]
rs11264987	0.97[ASN][1000 genomes]
rs11264988	0.97[ASN][1000 genomes]
rs11264989	0.91[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11264994	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11264997	0.96[ASN][1000 genomes]
rs11264998	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs11265002	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs11265003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1157523	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1157525	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12034004	0.97[ASN][1000 genomes]
rs12041218	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12044283	0.97[ASN][1000 genomes]
rs12044288	0.97[ASN][1000 genomes]
rs12075903	0.99[ASN][1000 genomes]
rs12078065	0.97[ASN][1000 genomes]
rs12080815	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12081915	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12118446	0.95[ASN][1000 genomes]
rs12122663	0.93[ASN][1000 genomes]
rs12133791	0.93[ASN][1000 genomes]
rs12133794	0.93[ASN][1000 genomes]
rs12145401	0.95[ASN][1000 genomes]
rs12403685	1.00[ASN][1000 genomes]
rs1342946	1.00[ASN][1000 genomes]
rs1342947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1342949	0.90[ASN][1000 genomes]
rs1342950	0.97[ASN][1000 genomes]
rs1342952	0.97[ASN][1000 genomes]
rs1342953	0.97[ASN][1000 genomes]
rs1342954	0.97[ASN][1000 genomes]
rs1342958	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs1418844	0.99[ASN][1000 genomes]
rs1418845	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1418846	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1418847	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1491196	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1573519	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs1578761	0.95[ASN][1000 genomes]
rs1578762	0.95[ASN][1000 genomes]
rs1578763	0.95[ASN][1000 genomes]
rs17630699	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1873509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1873510	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1873511	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1894038	1.00[ASN][1000 genomes]
rs1894040	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2023632	0.99[ASN][1000 genomes]
rs2051450	0.95[ASN][1000 genomes]
rs2051451	0.97[ASN][1000 genomes]
rs2157687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2157689	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2213947	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2220633	1.00[ASN][1000 genomes]
rs2317969	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2317970	0.93[ASN][1000 genomes]
rs2873593	0.93[ASN][1000 genomes]
rs2873594	0.93[ASN][1000 genomes]
rs2873595	0.93[ASN][1000 genomes]
rs4276920	0.93[ASN][1000 genomes]
rs4373761	0.97[ASN][1000 genomes]
rs4575081	0.93[ASN][1000 genomes]
rs4609418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4614256	0.97[ASN][1000 genomes]
rs4657080	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs57366633	1.00[ASN][1000 genomes]
rs6427438	1.00[ASN][1000 genomes]
rs6427439	0.99[ASN][1000 genomes]
rs6657638	0.95[ASN][1000 genomes]
rs6663277	0.95[ASN][1000 genomes]
rs6664542	0.99[ASN][1000 genomes]
rs6666609	0.95[ASN][1000 genomes]
rs6670343	0.95[ASN][1000 genomes]
rs6672789	0.95[ASN][1000 genomes]
rs6674656	0.95[ASN][1000 genomes]
rs6679056	1.00[ASN][1000 genomes]
rs6689657	0.99[ASN][1000 genomes]
rs6697656	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs6699473	0.95[ASN][1000 genomes]
rs7512592	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs7514555	1.00[ASN][1000 genomes]
rs7514968	0.95[ASN][1000 genomes]
rs7515245	0.95[ASN][1000 genomes]
rs7518708	0.93[ASN][1000 genomes]
rs7518808	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7525362	0.95[ASN][1000 genomes]
rs7526514	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7533071	0.93[ASN][1000 genomes]
rs7540999	0.93[ASN][1000 genomes]
rs7548349	0.95[ASN][1000 genomes]
rs7549123	1.00[ASN][1000 genomes]
rs7549581	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7551497	1.00[ASN][1000 genomes]
rs7555174	0.96[ASN][1000 genomes]
rs863345	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs863346	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs863347	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs863351	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs863352	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs863353	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs863356	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs863365	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs879635	0.99[ASN][1000 genomes]
rs879637	0.99[ASN][1000 genomes]
rs923663	0.93[ASN][1000 genomes]
rs923664	0.93[ASN][1000 genomes]
rs949397	0.99[ASN][1000 genomes]
rs949398	0.99[ASN][1000 genomes]
rs950260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs950487	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9651046	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs9804005	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

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	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1418843	DCST2	cis	cerebellum	SCAN
rs1418843	LCE1A	cis	cerebellum	SCAN
rs1418843	FCRL2	cis	parietal	SCAN
rs1418843	CD5L	cis	parietal	SCAN
rs1418843	IGSF8	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158444200-158456600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:158449600-158451200	Genic enhancers	Thymus	Thymus
3	chr1:158449600-158451200	Genic enhancers	Dnd41	blood
4	chr1:158450000-158451400	Genic enhancers	Fetal Thymus	thymus

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