Variant report

Variant	rs540431
Chromosome Location	chr1:57859521-57859522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10047071	0.91[CHB][hapmap];0.96[CHD][hapmap]
rs10047072	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10047073	0.91[CHB][hapmap];0.96[CHD][hapmap]
rs10047177	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10047179	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10493219	0.92[CHD][hapmap]
rs10493221	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1077424	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs10889036	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs10889037	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs10889038	0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs10889039	0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs10889041	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10889042	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs10889043	0.89[ASN][1000 genomes]
rs10889044	0.82[ASN][1000 genomes]
rs11207007	0.89[JPT][hapmap]
rs11207011	0.92[CHD][hapmap]
rs11207012	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs11207016	0.91[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs11207017	0.82[ASN][1000 genomes]
rs11207018	0.83[EUR][1000 genomes]
rs11207024	0.89[ASN][1000 genomes]
rs11207025	0.89[ASN][1000 genomes]
rs11207026	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11207027	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11207028	0.89[ASN][1000 genomes]
rs11207029	0.89[ASN][1000 genomes]
rs11585751	0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs11590708	0.91[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs11799925	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs11803514	0.89[ASN][1000 genomes]
rs12067263	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12087888	0.92[CHD][hapmap]
rs12092706	0.89[ASN][1000 genomes]
rs12119147	1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs12119210	0.91[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap]
rs12126723	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs12137169	0.92[CHD][hapmap];0.82[ASN][1000 genomes]
rs12139429	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs12240237	0.91[CHB][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs1240442	0.82[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1240443	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12405761	0.90[CHB][hapmap]
rs12565446	0.91[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs12565636	0.80[EUR][1000 genomes]
rs12741210	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs1424462	0.90[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs1424463	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1424464	0.91[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs1424465	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs1424466	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs1424467	0.91[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap]
rs1424469	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs1504594	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs1557222	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs166514	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs17115686	0.92[CHD][hapmap]
rs17115750	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17423255	0.91[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs17424216	0.92[CHD][hapmap]
rs17425017	0.92[CHD][hapmap]
rs17456661	0.84[CHD][hapmap]
rs17458730	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs17459384	0.82[ASN][1000 genomes]
rs1778032	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1834151	0.91[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes]
rs1862925	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs2113453	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2216808	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs2405696	0.91[CHB][hapmap]
rs2405697	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2405994	0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs267638	0.88[CHD][hapmap]
rs267647	0.88[CHD][hapmap]
rs267650	0.92[CHD][hapmap]
rs267651	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap]
rs269038	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs269039	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs269042	0.83[ASW][hapmap];0.92[CEU][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs269044	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs269045	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs269048	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs269049	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs269050	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs269051	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs269054	0.89[ASN][1000 genomes]
rs269057	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3738553	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3844041	0.81[CHD][hapmap];0.89[ASN][1000 genomes]
rs3850549	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs3850550	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3850552	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3850556	0.84[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs3861833	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3861834	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs3896279	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs3909556	0.92[CHD][hapmap]
rs3909558	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs439378	0.88[CHD][hapmap]
rs4912247	0.89[ASN][1000 genomes]
rs499339	0.89[JPT][hapmap]
rs511115	0.89[ASN][1000 genomes]
rs515148	0.89[ASN][1000 genomes]
rs516918	0.89[ASN][1000 genomes]
rs517825	0.89[ASN][1000 genomes]
rs532926	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs563099	0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.89[ASN][1000 genomes]
rs563270	0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[ASN][1000 genomes]
rs564951	1.00[JPT][hapmap]
rs565032	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs566847	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs567773	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs574726	0.89[JPT][hapmap]
rs61769756	0.89[ASN][1000 genomes]
rs6587767	0.82[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap]
rs6587768	0.89[ASN][1000 genomes]
rs6665166	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6687842	0.82[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]
rs6687934	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.81[ASN][1000 genomes]
rs736109	0.88[CHD][hapmap]
rs746937	0.88[CHD][hapmap]
rs7513076	0.82[CHB][hapmap]
rs7535763	0.90[CHB][hapmap];0.96[CHD][hapmap]
rs90940	0.92[CHB][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap]

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	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv954	chr1:57823140-57865799	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57848000-57859800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:57855200-57862000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:57856400-57863200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr1:57858000-57868600	Weak transcription	Fetal Brain Male	brain
5	chr1:57859400-57860200	Enhancers	Fetal Intestine Small	intestine

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