Variant report

Variant	rs2712516
Chromosome Location	chr12:59152365-59152366
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1353610	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1353611	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1531138	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2605422	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2645865	1.00[EUR][1000 genomes]
rs2645866	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2645867	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712503	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712504	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712505	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712506	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712508	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2712510	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712511	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712513	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712514	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712515	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2712517	0.94[AMR][1000 genomes];1.00[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	esv2758311	chr12:59022729-59323045	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2759902	chr12:59022729-59323045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv1049807	chr12:59069437-59227711	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv826390	chr12:59097995-59199786	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1043385	chr12:59149582-59758952	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2712516	ZNF385A	cis	parietal	SCAN
rs2712516	CDK4	cis	cerebellum	SCAN
rs2712516	GTSF1	cis	cerebellum	SCAN
rs2712516	TARBP2	cis	parietal	SCAN
rs2712516	IFI44L	trans	brain	seeQTL
rs2712516	STAT1	trans	brain	seeQTL
rs2712516	SMUG1	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:59150600-59152400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:59150600-59152600	Enhancers	HUVEC	blood vessel
3	chr12:59151600-59156800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:59151800-59152600	Enhancers	NHEK	skin
5	chr12:59152000-59152600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:59152000-59157600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:59152200-59157400	Weak transcription	NHLF	lung
8	chr12:59152200-59157600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:59152200-59158000	Weak transcription	HSMM	muscle
10	chr12:59152200-59158200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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