Variant report

Variant	rs12812570
Chromosome Location	chr12:48005034-48005035
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11168170	0.82[EUR][1000 genomes]
rs11168177	0.84[EUR][1000 genomes]
rs11832890	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12229373	0.82[EUR][1000 genomes]
rs12422983	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs12423645	1.00[JPT][hapmap]
rs12809264	0.84[EUR][1000 genomes]
rs12818212	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs2077621	0.80[EUR][1000 genomes]
rs71445738	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
2	nsv832400	chr12:47840248-48024605	Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv430507	chr12:47883933-48079507	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1051131	chr12:47883981-48016556	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv899056	chr12:47940764-48012390	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv558786	chr12:47942029-48044011	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv558788	chr12:47945797-48012390	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	esv2761737	chr12:47946795-48045722	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1053061	chr12:47946795-48045722	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv899057	chr12:47947551-48012390	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv527728	chr12:47954597-48044506	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12812570	RAPGEF3	cis	parietal	SCAN
rs12812570	RAPGEF3	cis	cerebellum	SCAN
rs12812570	PUS7L	cis	parietal	SCAN
rs12812570	TMEM117	cis	cerebellum	SCAN
rs12812570	ISOC2	trans	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47992600-48006600	Weak transcription	HSMMtube	muscle
2	chr12:47996000-48006800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:47998800-48030800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:47999600-48006400	Weak transcription	Primary T cells from cord blood	blood
5	chr12:48001800-48006800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:48002000-48005800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr12:48002000-48006800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:48002600-48005800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:48002600-48006400	Weak transcription	Primary B cells from cord blood	blood
10	chr12:48003600-48006000	Enhancers	Fetal Muscle Leg	muscle
11	chr12:48004000-48006000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:48004400-48005600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:48005000-48005200	Enhancers	Colon Smooth Muscle	Colon

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

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