Variant report

Variant	rs12495621
Chromosome Location	chr3:157917351-157917352
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	chr3:157907378..157909218-chr3:157917201..157920072,2	K562	blood:

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10513526	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs10936138	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs12486445	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12487397	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs12487873	0.87[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap]
rs12490116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12493633	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12497109	0.85[EUR][1000 genomes]
rs12497273	0.85[EUR][1000 genomes]
rs12634372	0.84[EUR][1000 genomes]
rs12634405	0.85[EUR][1000 genomes]
rs12634483	0.83[EUR][1000 genomes]
rs12635395	0.83[EUR][1000 genomes]
rs12638258	0.87[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap]
rs1320239	0.87[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap]
rs17486183	0.83[EUR][1000 genomes]
rs17683721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs17683787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs2140982	0.83[EUR][1000 genomes]
rs2176890	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2362247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28781280	0.85[EUR][1000 genomes]
rs4432589	0.83[EUR][1000 genomes]
rs4542974	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs55638807	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55818809	0.85[EUR][1000 genomes]
rs56019559	0.83[EUR][1000 genomes]
rs59661293	0.83[EUR][1000 genomes]
rs60566034	0.83[EUR][1000 genomes]
rs61244743	0.88[EUR][1000 genomes]
rs73164073	0.82[AMR][1000 genomes]
rs73164083	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73164088	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73164089	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73164094	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166303	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166305	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73166307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73166311	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73166326	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166328	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73166334	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73166338	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73166343	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73166347	0.85[EUR][1000 genomes]
rs73166351	0.83[EUR][1000 genomes]
rs73166352	0.85[EUR][1000 genomes]
rs73166357	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73166361	0.82[EUR][1000 genomes]
rs73166362	0.85[EUR][1000 genomes]
rs73166370	0.85[EUR][1000 genomes]
rs73166374	0.85[EUR][1000 genomes]
rs73166375	0.85[EUR][1000 genomes]
rs73166381	0.85[EUR][1000 genomes]
rs73166383	0.85[EUR][1000 genomes]
rs73166386	0.85[EUR][1000 genomes]
rs73166387	0.85[EUR][1000 genomes]
rs73166388	0.85[EUR][1000 genomes]
rs73166390	0.85[EUR][1000 genomes]
rs73166394	0.83[EUR][1000 genomes]
rs73166397	0.83[EUR][1000 genomes]
rs73166399	0.83[EUR][1000 genomes]
rs73168703	0.83[EUR][1000 genomes]
rs73168704	0.83[EUR][1000 genomes]
rs73168713	0.83[EUR][1000 genomes]
rs73168718	0.83[EUR][1000 genomes]
rs73168720	0.83[EUR][1000 genomes]
rs73168737	0.83[EUR][1000 genomes]
rs7650062	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs951113	0.83[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12495621	GFM1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157889800-157918600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:157914200-157984400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:157914800-157921200	Weak transcription	Pancreas	Pancrea
4	chr3:157916000-157918800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:157916400-157919200	ZNF genes & repeats	Dnd41	blood
6	chr3:157916600-157917400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
7	chr3:157916600-157917600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:157917000-157926200	Weak transcription	Ovary	ovary

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