Variant report

Variant	rs2128535
Chromosome Location	chr3:156789192-156789193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156786906..156789302-chr3:156835545..156837203,2	K562	blood:
2	chr3:156392417..156394296-chr3:156787392..156790127,2	K562	blood:

Variant related genes	Relation type
ENSG00000163659	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1032041	0.80[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs1032044	0.82[JPT][hapmap]
rs10936054	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs10936055	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs11715321	0.83[CHD][hapmap];0.94[JPT][hapmap]
rs11719102	0.81[ASN][1000 genomes]
rs11720579	0.80[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs12636741	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs13082176	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs1384541	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs1482854	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs1482855	0.80[CHB][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs1482856	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs1482857	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs1600978	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs1842840	0.80[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap]
rs2046269	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs4263246	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs4479548	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680332	0.94[JPT][hapmap]
rs4680337	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6799034	0.80[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs7612970	0.81[JPT][hapmap]
rs7616314	0.80[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap]
rs7624328	0.82[JPT][hapmap]
rs931245	0.80[ASN][1000 genomes]
rs9811993	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs9812759	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9859727	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs9867766	0.80[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2128535	VEPH1	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156782400-156794000	Weak transcription	Right Atrium	heart
2	chr3:156782600-156795000	Weak transcription	Fetal Heart	heart
3	chr3:156782800-156789400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:156782800-156795000	Weak transcription	Adipose Nuclei	Adipose
5	chr3:156783400-156793400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:156785200-156791400	Weak transcription	NHLF	lung
7	chr3:156785200-156791600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:156785200-156791600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:156785200-156791600	Weak transcription	Brain Substantia Nigra	brain
10	chr3:156785200-156793400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:156785400-156789600	Weak transcription	GM12878-XiMat	blood
12	chr3:156786000-156791600	Weak transcription	NH-A	brain
13	chr3:156787600-156789200	Enhancers	Liver	Liver
14	chr3:156787600-156789200	Enhancers	Fetal Intestine Large	intestine
15	chr3:156787800-156789200	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr3:156787800-156789200	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr3:156788000-156789200	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr3:156788000-156789800	Enhancers	Brain Hippocampus Middle	brain
19	chr3:156788200-156794800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:156788400-156789200	Enhancers	Fetal Thymus	thymus
21	chr3:156788600-156789200	Enhancers	Sigmoid Colon	Sigmoid Colon
22	chr3:156788600-156790800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:156788800-156791600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr3:156788800-156793600	Weak transcription	HSMM	muscle
25	chr3:156789000-156789400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:156789000-156791400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:156789000-156791400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:156789000-156791400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:156789000-156791400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:156789000-156791400	Weak transcription	NHDF-Ad	bronchial
31	chr3:156789000-156791600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:156789000-156791600	Weak transcription	Brain Anterior Caudate	brain
33	chr3:156789000-156791800	Weak transcription	Pancreas	Pancrea
34	chr3:156789000-156793200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:156789000-156793400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:156789000-156793400	Weak transcription	Osteobl	bone
37	chr3:156789000-156805000	Weak transcription	Aorta	Aorta

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