Variant report

Variant	rs7673867
Chromosome Location	chr4:110278483-110278484
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COL25A1-1	chr4:110278435-110278537	ENSG00000247950
2	lnc-COL25A1-1	chr4:110278199-110278716	ENSG00000247950

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10002595	0.81[CHD][hapmap];0.88[MEX][hapmap]
rs10005198	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10007410	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10016533	0.88[MEX][hapmap]
rs10155246	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11098033	0.90[CHD][hapmap]
rs11098035	0.86[CHD][hapmap]
rs11929713	0.86[MEX][hapmap]
rs11933172	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11939924	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11942858	0.81[CHD][hapmap];0.86[MEX][hapmap]
rs12641197	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12641272	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12643055	0.81[CHD][hapmap]
rs12648965	0.81[CHD][hapmap]
rs12650654	0.90[CHD][hapmap]
rs13103034	0.81[CHD][hapmap];0.86[MEX][hapmap]
rs13104799	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13110999	0.86[MEX][hapmap]
rs13113384	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13119700	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13122093	0.86[MEX][hapmap]
rs13123618	0.81[CHD][hapmap];0.88[MEX][hapmap]
rs13126829	0.90[EUR][1000 genomes]
rs13128445	1.00[MEX][hapmap]
rs13138833	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13140373	0.86[MEX][hapmap]
rs13142698	0.85[CHD][hapmap];0.88[MEX][hapmap]
rs13145066	0.81[CHD][hapmap];0.86[MEX][hapmap]
rs1557804	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17040436	0.81[CHD][hapmap];0.86[MEX][hapmap]
rs17040439	0.81[CHD][hapmap];0.86[MEX][hapmap]
rs17040461	0.81[CHD][hapmap];0.86[MEX][hapmap]
rs17842269	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1859144	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1859146	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1859147	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1981540	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1981541	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2079107	0.83[ASN][1000 genomes]
rs2079108	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2214377	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2346014	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28374470	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28463999	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28542804	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28585579	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28628718	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28681408	0.81[CHD][hapmap];0.88[MEX][hapmap]
rs28749845	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4524460	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60369504	0.83[ASN][1000 genomes]
rs6533426	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6533434	0.88[MEX][hapmap]
rs6818911	0.81[CHD][hapmap];0.88[MEX][hapmap]
rs6825928	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs6827985	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6835683	0.81[CHD][hapmap];0.88[MEX][hapmap]
rs6841133	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6841198	0.81[CHD][hapmap];0.88[MEX][hapmap]
rs6841222	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs714586	0.86[MEX][hapmap]
rs7436583	0.90[CHD][hapmap];0.88[MEX][hapmap]
rs7436745	0.90[CHD][hapmap]
rs7665024	0.90[EUR][1000 genomes]
rs7673595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs7675344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7675602	0.81[CHD][hapmap];0.88[MEX][hapmap]
rs7680752	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7680920	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7684744	0.94[EUR][1000 genomes]
rs7685787	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7694523	0.90[EUR][1000 genomes]
rs7695754	1.00[CEU][hapmap]
rs7699247	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs876464	0.94[EUR][1000 genomes]
rs9307329	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9985632	0.81[CHD][hapmap]
rs9993228	0.94[EUR][1000 genomes]
rs9994676	0.81[CHD][hapmap]
rs9996165	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9996432	0.94[EUR][1000 genomes]
rs9996537	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9996920	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9999270	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9999278	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9999570	0.81[CHD][hapmap];0.88[MEX][hapmap]
rs9999751	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110278200-110279600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
2	chr4:110278200-110282200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:110278400-110278800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
4	chr4:110278400-110281600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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