Variant report

Variant	rs1456093
Chromosome Location	chr3:157216553-157216554
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:157216420-157216570	AoAF	blood vessel:	n/a	n/a
2	POLR2A	chr3:157216500-157218110	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:157206354..157208602-chr3:157216445..157218072,2	MCF-7	breast:
2	chr3:157189468..157191682-chr3:157215213..157216776,2	MCF-7	breast:
3	chr3:157211587..157213759-chr3:157215822..157218040,2	K562	blood:
4	chr3:156877312..156878829-chr3:157215828..157217398,2	MCF-7	breast:

No data

Variant related genes	Relation type
VEPH1	TF binding region
ENSG00000163660	Chromatin interaction
ENSG00000197415	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11718199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11923106	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12485456	0.82[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13318762	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1350150	0.96[CEU][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1378797	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1378802	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1456094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1456095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1456112	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1456113	0.82[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1550651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1840667	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1988267	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2034094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2316349	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2840046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4679800	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680373	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7626974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7629184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs920759	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs973207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9809137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs988758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1456093	ARL14	cis	parietal	SCAN
rs1456093	C3orf55	cis	cerebellum	SCAN
rs1456093	C3orf55	cis	parietal	SCAN
rs1456093	VEPH1	cis	cerebellum	SCAN
rs1456093	PTX3	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157194600-157217000	Weak transcription	Pancreas	Pancrea
2	chr3:157210600-157217000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr3:157212000-157216600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr3:157212200-157217200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:157212600-157216800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:157212600-157217000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:157212800-157217000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:157212800-157217000	Weak transcription	NHLF	lung
9	chr3:157213200-157216800	Weak transcription	HSMM	muscle
10	chr3:157213200-157217000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:157213200-157217000	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:157213200-157217000	Weak transcription	NH-A	brain
13	chr3:157213200-157217200	Weak transcription	HSMMtube	muscle
14	chr3:157213200-157221200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:157213400-157217000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:157213800-157217200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:157214000-157216800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr3:157214000-157216800	Weak transcription	Adipose Nuclei	Adipose
19	chr3:157214000-157217200	Weak transcription	HUVEC	blood vessel
20	chr3:157214200-157217000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:157214800-157216600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:157215200-157217800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:157215400-157217200	Weak transcription	Osteobl	bone
24	chr3:157216000-157217000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:157216200-157216600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:157216200-157216600	Enhancers	NHDF-Ad	bronchial
27	chr3:157216200-157216800	Enhancers	H1 Cell Line	embryonic stem cell
28	chr3:157216200-157216800	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr3:157216200-157217000	Enhancers	H9 Cell Line	embryonic stem cell
30	chr3:157216200-157217000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:157216200-157217000	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr3:157216200-157217000	Enhancers	Fetal Kidney	kidney
33	chr3:157216200-157217000	Enhancers	Fetal Lung	lung
34	chr3:157216200-157217200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:157216200-157217200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:157216200-157217800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:157216400-157216600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
38	chr3:157216400-157216600	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr3:157216400-157216600	Enhancers	Hela-S3	cervix
40	chr3:157216400-157216800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:157216400-157216800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
42	chr3:157216400-157217200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:157216400-157217200	Enhancers	Cortex derived primary cultured neurospheres	brain

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