Variant report

Variant	rs6475046
Chromosome Location	chr9:16386852-16386853
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4612476	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4620378	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4961487	0.82[ASN][1000 genomes]
rs9298762	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9406636	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9407769	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429999	chr9:16102066-16389100	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv892644	chr9:16275107-16389006	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv466264	chr9:16359608-16390629	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
6	nsv613669	chr9:16359608-16390629	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS	lncRNA	n/a	inside rSNPs	diseases
7	esv2762798	chr9:16385811-16389383	Enhancers Flanking Active TSS Weak transcription Genic enhancers	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6475046	MPDZ	cis	cerebellum	SCAN
rs6475046	RPS6	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16385200-16387000	Enhancers	NHDF-Ad	bronchial
2	chr9:16385400-16387000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:16385400-16387000	Enhancers	Osteobl	bone
4	chr9:16385600-16387000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:16386000-16387000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:16386000-16387000	Enhancers	HMEC	breast
7	chr9:16386200-16387000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr9:16386200-16387200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:16386200-16388600	Weak transcription	Fetal Stomach	stomach
10	chr9:16386400-16387000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:16386400-16387000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:16386400-16387000	Enhancers	Hela-S3	cervix

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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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