Variant report

Variant	rs16827792
Chromosome Location	chr3:157245912-157245913
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:157240973..157243673-chr3:157244853..157247199,2	K562	blood:
2	chr3:157240375..157243195-chr3:157245834..157247869,2	K562	blood:
3	chr3:157244287..157247060-chr3:157247713..157249691,2	MCF-7	breast:
4	chr3:157244064..157246692-chr3:157247762..157250308,3	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12485399	0.94[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs12489204	1.00[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs12492543	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs12493333	0.83[ASN][1000 genomes]
rs12494755	0.88[CHB][hapmap];0.84[JPT][hapmap]
rs12498099	1.00[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs16827862	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs2034093	0.83[ASN][1000 genomes]
rs2083818	0.83[ASN][1000 genomes]
rs3749293	1.00[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs60734635	0.87[ASN][1000 genomes]
rs60849513	0.84[ASN][1000 genomes]
rs62278667	0.85[ASN][1000 genomes]
rs6766351	1.00[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs6783699	0.81[ASN][1000 genomes]
rs6798962	0.83[ASN][1000 genomes]
rs6804345	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16827792	VEPH1	cis	cerebellum	SCAN
rs16827792	C3orf55	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157243400-157246600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:157243600-157246600	Enhancers	Muscle Satellite Cultured Cells	--
3	chr3:157244200-157246600	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr3:157244600-157246600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:157244600-157246800	Genic enhancers	HUVEC	blood vessel
6	chr3:157244800-157246000	Enhancers	HSMMtube	muscle
7	chr3:157244800-157246600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:157244800-157246600	Enhancers	Brain Germinal Matrix	brain
9	chr3:157244800-157246600	Enhancers	HSMM	muscle
10	chr3:157244800-157246600	Enhancers	NH-A	brain
11	chr3:157244800-157246600	Enhancers	NHLF	lung
12	chr3:157244800-157246800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:157244800-157248600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:157245000-157246000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:157245000-157246000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:157245000-157246000	Weak transcription	Fetal Brain Male	brain
17	chr3:157245000-157246600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:157245000-157246600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr3:157245000-157246600	Enhancers	Fetal Lung	lung
20	chr3:157245200-157246600	Enhancers	Ovary	ovary
21	chr3:157245400-157246000	Flanking Active TSS	Osteobl	bone
22	chr3:157245400-157248800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:157245600-157246000	Weak transcription	Fetal Heart	heart
24	chr3:157245800-157246000	Enhancers	Fetal Brain Female	brain
25	chr3:157245800-157246600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:157245800-157246600	Enhancers	Right Atrium	heart
27	chr3:157245800-157247000	Enhancers	NHDF-Ad	bronchial

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