Variant report

Variant	rs12488037
Chromosome Location	chr3:160882514-160882515
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160880908..160883416-chr3:160895673..160897836,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs12488318	0.80[AMR][1000 genomes]
rs12494844	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13318781	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13319969	0.85[AMR][1000 genomes]
rs13320863	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1599380	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1599391	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1947685	0.95[EUR][1000 genomes]
rs1970834	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35152606	0.95[EUR][1000 genomes]
rs35446590	0.93[EUR][1000 genomes]
rs36105583	0.95[EUR][1000 genomes]
rs4270539	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4429651	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4487256	0.81[ASN][1000 genomes]
rs4490410	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62278031	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62278055	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62279860	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62279861	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs62279862	0.80[AMR][1000 genomes]
rs731363	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73160351	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73160362	0.81[ASN][1000 genomes]
rs7634115	0.87[AMR][1000 genomes]
rs9290067	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9290068	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9290072	0.90[ASN][1000 genomes]
rs9810737	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9817747	0.85[ASN][1000 genomes]
rs9818516	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9824501	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9825118	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9827833	0.80[AMR][1000 genomes]
rs9828205	0.93[EUR][1000 genomes]
rs9828231	0.80[AMR][1000 genomes]
rs9831725	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9836074	0.95[EUR][1000 genomes]
rs9836094	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9842281	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9857946	0.90[ASN][1000 genomes]
rs9858399	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9862258	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9878365	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12488037	DNMT1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160880800-160883200	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:160881000-160886400	Weak transcription	Fetal Heart	heart
3	chr3:160881200-160884200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:160881800-160883200	ZNF genes & repeats	NHLF	lung
5	chr3:160882000-160883400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:160882000-160883400	ZNF genes & repeats	Osteobl	bone
7	chr3:160882400-160882600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:160882400-160883200	Strong transcription	Ovary	ovary
9	chr3:160882400-160883200	ZNF genes & repeats	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links