Variant report

Variant	rs1074864
Chromosome Location	chr3:157132577-157132578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1014855	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10755111	0.85[JPT][hapmap]
rs10936077	0.81[JPT][hapmap]
rs10936088	0.88[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10936089	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1403105	0.85[JPT][hapmap]
rs1456104	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1456109	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2316712	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2321743	0.85[JPT][hapmap]
rs3911402	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679790	0.85[JPT][hapmap]
rs4679791	0.85[JPT][hapmap]
rs4680353	0.85[JPT][hapmap]
rs722485	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9831686	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9837655	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848774	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1074864	VEPH1	cis	cerebellum	SCAN
rs1074864	PTX3	cis	cerebellum	SCAN
rs1074864	C3orf55	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157091800-157142600	Weak transcription	Pancreas	Pancrea
2	chr3:157119000-157142800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:157120000-157142600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:157120200-157135800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:157123000-157135000	Weak transcription	Spleen	Spleen
6	chr3:157124400-157134200	Weak transcription	HSMM	muscle
7	chr3:157124400-157135800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:157124600-157134800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:157126600-157135400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:157127000-157141800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr3:157127400-157134200	Weak transcription	NHLF	lung
12	chr3:157128200-157138600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:157129000-157135000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:157130000-157135000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:157130000-157135000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:157130600-157134200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:157130800-157135000	Weak transcription	HSMMtube	muscle
18	chr3:157131600-157134800	Weak transcription	Osteobl	bone
19	chr3:157131600-157135000	Weak transcription	NH-A	brain
20	chr3:157131800-157133600	Weak transcription	HUVEC	blood vessel
21	chr3:157131800-157134800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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