Variant report

Variant	rs12525547
Chromosome Location	chr6:45692933-45692934
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10948245	1.00[YRI][hapmap]
rs12665312	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16873698	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1932040	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs321321	0.87[CHB][hapmap]
rs9349326	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9369573	0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9381394	0.99[EUR][1000 genomes]
rs9395112	0.90[CEU][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12525547	ABCC10	cis	cerebellum	SCAN
rs12525547	CAPN11	cis	parietal	SCAN
rs12525547	CUL7	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45692200-45693000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:45692200-45693000	Enhancers	NHDF-Ad	bronchial
3	chr6:45692400-45693000	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:45692600-45693000	Enhancers	Fetal Stomach	stomach
5	chr6:45692600-45693000	Enhancers	Hela-S3	cervix
6	chr6:45692600-45695600	Weak transcription	Fetal Muscle Leg	muscle
7	chr6:45692800-45695000	Weak transcription	Fetal Heart	heart
8	chr6:45692800-45695600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr6:45692800-45695800	Weak transcription	HMEC	breast
10	chr6:45692800-45696400	Weak transcription	Fetal Lung	lung
11	chr6:45692800-45696400	Weak transcription	HSMMtube	muscle
12	chr6:45692800-45696400	Weak transcription	NHEK	skin
13	chr6:45692800-45696400	Weak transcription	Osteobl	bone

Quick Search:

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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