Variant report

Variant	rs3774558
Chromosome Location	chr3:53775739-53775740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11719163	0.83[AMR][1000 genomes]
rs11918583	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs1573818	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs28365115	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3774567	0.83[ASN][1000 genomes]
rs3821847	1.00[LWK][hapmap]
rs3821866	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs3846215	0.85[AMR][1000 genomes]
rs41276449	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs56384446	0.83[ASN][1000 genomes]
rs714786	0.83[AMR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv1002452	chr3:53742148-53802811	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv520027	chr3:53762713-53784625	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3774558	NPRL2	cis	parietal	SCAN
rs3774558	RBM5	cis	parietal	SCAN
rs3774558	ABHD14B	cis	parietal	SCAN
rs3774558	ACTR8	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53742600-53778000	Weak transcription	Pancreas	Pancrea
2	chr3:53761600-53781800	Weak transcription	Spleen	Spleen
3	chr3:53764200-53779800	Weak transcription	Liver	Liver
4	chr3:53764800-53783400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:53765000-53779800	Weak transcription	Brain Anterior Caudate	brain
6	chr3:53765000-53779800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:53765000-53788600	Weak transcription	Fetal Kidney	kidney
8	chr3:53765200-53783400	Weak transcription	Brain Angular Gyrus	brain
9	chr3:53765400-53781600	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:53766600-53781200	Weak transcription	Lung	lung
11	chr3:53768600-53801000	Strong transcription	Fetal Lung	lung
12	chr3:53769600-53787400	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:53770200-53779800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:53773000-53775800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:53773000-53807600	Strong transcription	Fetal Intestine Large	intestine
16	chr3:53774200-53776800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:53774200-53789200	Weak transcription	Fetal Brain Male	brain
18	chr3:53774400-53782000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:53774600-53785000	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:53774800-53775800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:53774800-53776400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:53774800-53807200	Strong transcription	Fetal Intestine Small	intestine

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