Variant report

Variant	rs2175779
Chromosome Location	chr4:21852429-21852430
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	chr4:21851861..21853893-chr4:21856339..21858880,2	K562	blood:
2	chr4:21843638..21845435-chr4:21850598..21852642,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR125-2	chr4:21844963-21854811	UM9-5
2	lnc-GPR125-2	chr4:21844964-21854811	NONHSAT095745

Variant related genes	Relation type
ENSG00000185774	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs10021133	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs10029040	0.85[ASN][1000 genomes]
rs1040039	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10516398	1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs10516400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10516407	0.88[CHB][hapmap];0.81[CHD][hapmap]
rs10805230	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10938854	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10938860	0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723231	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11725029	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs11725506	0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11725634	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs11728958	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11730531	0.82[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs11731098	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11731835	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs11732527	0.85[CHB][hapmap];0.86[CHD][hapmap]
rs11734604	1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs11736882	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11737531	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs11931923	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11938269	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11943445	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs11944162	1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs12503772	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12512545	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12512603	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13104527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13105122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13105154	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13110177	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs13112610	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13115987	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs13119994	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13128189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13129819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13132296	0.92[ASN][1000 genomes]
rs13135188	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13135698	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13141904	0.92[ASN][1000 genomes]
rs13142511	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13143578	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13146273	0.85[ASN][1000 genomes]
rs13147352	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs1380271	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.81[TSI][hapmap];0.85[ASN][1000 genomes]
rs1380272	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs1398835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1459279	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1459280	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs168626	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17496681	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs17496959	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17497844	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17497900	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17498614	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17561951	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs17563311	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs17563769	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17563824	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs17564865	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17566434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17570050	0.88[CHB][hapmap]
rs17570140	0.86[CHB][hapmap]
rs181718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1824368	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs1841187	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1841188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1847426	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs1847427	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs184860	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2044809	1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs2137650	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2175780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2323128	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34008037	0.90[ASN][1000 genomes]
rs34099045	0.85[ASN][1000 genomes]
rs34375823	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34708714	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34839938	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34945659	0.85[ASN][1000 genomes]
rs35146316	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35161937	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35175333	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35215732	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35489277	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35719625	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35733545	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35827665	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35842590	0.85[ASN][1000 genomes]
rs35921228	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35937671	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs360697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs360698	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4455402	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4618303	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4631029	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696989	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4697243	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57134420	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57505034	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60628330	0.85[ASN][1000 genomes]
rs6448076	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6448091	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6448096	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6814698	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6819627	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6823352	0.88[CHB][hapmap]
rs6830224	0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6834778	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6837235	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6839725	0.88[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6839776	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6852952	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6853293	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71607091	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs71607093	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71607096	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7656546	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7659552	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7661087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7662958	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7684151	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs7695756	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9884203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9884843	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9995230	0.85[EUR][1000 genomes];0.95[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	nsv817467	chr4:21602921-22422816	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:21849800-21854400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:21850600-21854200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr4:21852400-21852800	Flanking Active TSS	Ovary	ovary

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