Variant report

Variant	rs9976018
Chromosome Location	chr21:40019129-40019130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs458465	0.83[CEU][hapmap]
rs464519	0.83[CEU][hapmap]
rs4817954	0.87[CEU][hapmap];0.83[CHD][hapmap]
rs62217511	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6517474	0.87[CEU][hapmap];0.81[CHD][hapmap];0.94[LWK][hapmap];0.80[MKK][hapmap];0.83[YRI][hapmap]
rs9976458	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9979888	0.83[CEU][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs9981408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065541	chr21:40009959-40024976	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1057719	chr21:40009959-40025433	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1058663	chr21:40009959-40031681	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1055287	chr21:40013735-40031681	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9976018	PLAC4	cis	parietal	SCAN
rs9976018	ATP5O	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40016000-40027000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr21:40016200-40024000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:40017000-40019200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr21:40017200-40019200	Enhancers	HSMMtube	muscle
5	chr21:40017200-40020000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr21:40018600-40019200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr21:40018600-40020600	Active TSS	Aorta	Aorta
8	chr21:40018800-40019200	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr21:40018800-40019200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr21:40018800-40019200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr21:40018800-40019200	Bivalent Enhancer	HSMM	muscle
12	chr21:40018800-40019200	Enhancers	Osteobl	bone
13	chr21:40019000-40019200	Bivalent Enhancer	NH-A	brain
14	chr21:40019000-40019200	Bivalent Enhancer	NHDF-Ad	bronchial
15	chr21:40019000-40019400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr21:40019000-40019600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr21:40019000-40019600	Enhancers	HMEC	breast
18	chr21:40019000-40019600	Enhancers	NHEK	skin
19	chr21:40019000-40020000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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