Variant report

Variant	rs6441133
Chromosome Location	chr3:157219947-157219948
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr3:157219781-157220003	H1-hESC	embryonic stem cell:	n/a	chr3:157219804-157219813
2	TEAD4	chr3:157219697-157220008	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156891687..156894320-chr3:157219306..157221888,3	MCF-7	breast:

Variant related genes	Relation type
VEPH1	TF binding region
ENSG00000222675	Chromatin interaction
ENSG00000243176	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12494965	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12496305	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12634385	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12634412	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12635273	0.80[CHB][hapmap]
rs1350149	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1378801	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16827688	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16827707	0.91[YRI][hapmap]
rs16827716	0.95[YRI][hapmap]
rs16827747	0.95[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2165873	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2316337	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2316348	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34316188	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4258914	0.81[CHB][hapmap]
rs4679797	1.00[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4680369	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4680371	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680372	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56877658	0.80[AFR][1000 genomes]
rs62278653	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62278654	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62278655	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62280977	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62280978	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62280979	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62280980	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62280981	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67228252	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6779693	0.81[CHB][hapmap]
rs73158530	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9682174	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6441133	VEPH1	cis	cerebellum	SCAN
rs6441133	C3orf55	cis	parietal	SCAN
rs6441133	C3orf33	cis	parietal	SCAN
rs6441133	RAD9A	trans	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157213200-157221200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:157217200-157220000	Enhancers	HUVEC	blood vessel
3	chr3:157217400-157222200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:157217800-157221000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:157217800-157235400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:157218000-157220800	Weak transcription	Fetal Brain Female	brain
7	chr3:157218000-157220800	Weak transcription	HSMM	muscle
8	chr3:157218000-157221600	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:157218200-157220000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:157218200-157220000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:157218200-157220000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:157218200-157220600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr3:157218200-157220800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr3:157218200-157220800	Weak transcription	HSMMtube	muscle
15	chr3:157218200-157221000	Weak transcription	Colonic Mucosa	Colon
16	chr3:157218200-157221000	Weak transcription	Pancreas	Pancrea
17	chr3:157218200-157221000	Weak transcription	NH-A	brain
18	chr3:157218200-157221600	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr3:157218400-157220800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr3:157218400-157220800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:157218400-157220800	Weak transcription	NHLF	lung
22	chr3:157218400-157221000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:157218400-157221000	Weak transcription	Osteobl	bone
24	chr3:157218800-157220800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:157218800-157220800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:157218800-157222200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:157219000-157222000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:157219200-157220800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:157219200-157220800	Active TSS	Brain Germinal Matrix	brain
30	chr3:157219200-157221400	Active TSS	Fetal Kidney	kidney
31	chr3:157219400-157221600	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr3:157219400-157221600	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr3:157219400-157221800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:157219600-157221000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr3:157219600-157221000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:157219600-157221400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr3:157219800-157220000	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr3:157219800-157220000	Bivalent Enhancer	Brain Substantia Nigra	brain
39	chr3:157219800-157220000	Flanking Active TSS	Fetal Lung	lung
40	chr3:157219800-157220800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:157219800-157221600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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