Variant report

Variant	rs12194357
Chromosome Location	chr6:119780014-119780015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2357379	0.80[EUR][1000 genomes]
rs35147613	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6927955	1.00[JPT][hapmap]
rs9320690	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9374796	0.81[AMR][1000 genomes];0.86[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	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1027904	chr6:119709488-120001986	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv533518	chr6:119712186-119998618	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3442553	chr6:119742069-120076777	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12194357	GPRC6A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119768200-119780400	Weak transcription	Aorta	Aorta
2	chr6:119776200-119789200	Weak transcription	Fetal Heart	heart
3	chr6:119777600-119784200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:119779600-119780400	Enhancers	Rectal Mucosa Donor 29	rectum
5	chr6:119779800-119780800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
6	chr6:119780000-119780800	Enhancers	Gastric	stomach
7	chr6:119780000-119781000	Enhancers	Duodenum Mucosa	Duodenum
8	chr6:119780000-119781000	Enhancers	Small Intestine	intestine
9	chr6:119780000-119781000	Enhancers	Stomach Mucosa	stomach
10	chr6:119780000-119781000	Flanking Active TSS	GM12878-XiMat	blood
11	chr6:119780000-119781400	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr6:119780000-119781800	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr6:119780000-119782000	Enhancers	Primary B cells from peripheral blood	blood

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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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