Variant report

Variant	rs860422
Chromosome Location	chr3:157915797-157915798
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 115 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10470472	0.85[EUR][1000 genomes]
rs1095636	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11717618	0.80[ASN][1000 genomes]
rs1193511	0.85[EUR][1000 genomes]
rs1193513	0.85[EUR][1000 genomes]
rs1193536	0.85[EUR][1000 genomes]
rs1204957	0.86[EUR][1000 genomes]
rs12485440	0.89[EUR][1000 genomes]
rs12486461	0.89[EUR][1000 genomes]
rs12696067	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13059066	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13061378	0.88[EUR][1000 genomes]
rs1581408	0.89[EUR][1000 genomes]
rs1608100	0.88[EUR][1000 genomes]
rs1608101	0.88[EUR][1000 genomes]
rs1609525	0.89[EUR][1000 genomes]
rs1609526	0.86[EUR][1000 genomes]
rs1610266	0.91[EUR][1000 genomes]
rs1610267	0.91[EUR][1000 genomes]
rs1610268	0.91[EUR][1000 genomes]
rs1724666	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1724679	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1729998	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1730008	0.84[EUR][1000 genomes]
rs1730029	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1730032	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1730039	0.85[EUR][1000 genomes]
rs1730041	0.84[EUR][1000 genomes]
rs1730044	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1730099	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1915935	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2682402	0.86[EUR][1000 genomes]
rs2682407	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2693540	0.86[EUR][1000 genomes]
rs2693546	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4261830	0.89[EUR][1000 genomes]
rs4317053	0.88[EUR][1000 genomes]
rs4346508	0.88[EUR][1000 genomes]
rs4414801	0.89[EUR][1000 genomes]
rs4431056	0.87[EUR][1000 genomes]
rs4602343	0.89[EUR][1000 genomes]
rs4622858	0.89[EUR][1000 genomes]
rs4642075	0.89[EUR][1000 genomes]
rs4680411	0.89[EUR][1000 genomes]
rs4680412	0.89[EUR][1000 genomes]
rs6441174	0.89[EUR][1000 genomes]
rs6762706	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6770442	0.83[EUR][1000 genomes]
rs6773505	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6789448	0.89[EUR][1000 genomes]
rs6790608	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6794461	0.88[EUR][1000 genomes]
rs6797626	0.88[EUR][1000 genomes]
rs6803532	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6803630	0.88[EUR][1000 genomes]
rs696715	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs698975	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs698976	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs698977	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs698979	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs698981	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs698982	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs698983	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs698984	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs698985	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs698992	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs699918	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs699923	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs699925	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs699926	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73164102	0.80[ASN][1000 genomes]
rs7614572	0.89[EUR][1000 genomes]
rs7618071	0.82[EUR][1000 genomes]
rs7622971	0.91[EUR][1000 genomes]
rs7630176	0.88[EUR][1000 genomes]
rs7647342	0.89[EUR][1000 genomes]
rs7653039	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs827104	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs827130	0.86[EUR][1000 genomes]
rs827139	0.86[EUR][1000 genomes]
rs827141	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827142	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827145	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs827146	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827147	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827149	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827153	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827155	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827157	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827160	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827162	0.85[EUR][1000 genomes]
rs827168	0.85[EUR][1000 genomes]
rs827170	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs827173	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs827174	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs827801	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs827805	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs844141	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs862352	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs864331	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs864876	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs866657	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9290020	0.86[EUR][1000 genomes]
rs9290021	0.89[EUR][1000 genomes]
rs9814942	0.89[EUR][1000 genomes]
rs9820954	0.89[EUR][1000 genomes]
rs9848433	0.86[EUR][1000 genomes]
rs9870745	0.84[EUR][1000 genomes]
rs9871021	0.83[EUR][1000 genomes]
rs9881063	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013391	chr3:157505943-158115553	Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv536775	chr3:157505943-158115553	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv829768	chr3:157832878-158012070	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv877689	chr3:157858930-158133307	Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs860422	RP11-538P18.2	cis	Nerve Tibial	GTEx
rs860422	RP11-538P18.2	cis	lung	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157868200-157916200	Weak transcription	Primary B cells from cord blood	blood
2	chr3:157887000-157916400	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr3:157889800-157918600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:157911200-157916400	Weak transcription	Dnd41	blood
5	chr3:157914200-157984400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:157914800-157921200	Weak transcription	Pancreas	Pancrea

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