Variant report

Variant	rs12376586
Chromosome Location	chr9:72648582-72648583
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10868350	0.80[ASN][1000 genomes]
rs10868395	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10868396	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12380611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12555472	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13287635	0.88[ASN][1000 genomes]
rs13290774	0.88[ASN][1000 genomes]
rs2975861	0.86[ASN][1000 genomes]
rs2997682	0.86[ASN][1000 genomes]
rs4237237	0.91[ASN][1000 genomes]
rs4397474	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4446788	0.91[ASN][1000 genomes]
rs4484763	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][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	nsv893438	chr9:72363992-72720438	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1049457	chr9:72539144-72765913	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv831613	chr9:72586058-72740061	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12376586	MAMDC2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72637600-72649200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr9:72646400-72650400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr9:72646600-72650400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:72646800-72648600	Weak transcription	NH-A	brain
5	chr9:72646800-72649000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr9:72646800-72649000	Weak transcription	Osteobl	bone
7	chr9:72646800-72649200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:72646800-72651000	Weak transcription	NHDF-Ad	bronchial
9	chr9:72646800-72651600	Weak transcription	HMEC	breast
10	chr9:72646800-72653000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:72646800-72653000	Weak transcription	HUVEC	blood vessel
12	chr9:72647000-72648600	Weak transcription	HSMM	muscle
13	chr9:72647000-72649000	Weak transcription	NHEK	skin
14	chr9:72647400-72657200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:72648000-72653000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr9:72648200-72650200	Enhancers	HSMMtube	muscle
17	chr9:72648400-72650200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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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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