Variant report

Variant	rs6740539
Chromosome Location	chr2:47004788-47004789
allele	G/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	RAD21	chr2:47003659-47004866	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000260977	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1009231	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs10168342	0.85[YRI][hapmap]
rs1345128	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1456009	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs1960838	0.84[ASN][1000 genomes]
rs4522653	0.85[YRI][hapmap]
rs6746471	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs6748938	0.85[YRI][hapmap]
rs6756738	0.92[CEU][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs897528	0.82[JPT][hapmap];0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv213378	chr2:47001834-47006121	Weak transcription Enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
7	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6740539	PIGF	cis	multi-tissue	Pritchard

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46981400-47006800	Weak transcription	Psoas Muscle	Psoas
2	chr2:46985600-47008200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:46987400-47005600	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:46987400-47005600	Weak transcription	Left Ventricle	heart
5	chr2:46987600-47006000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:46992400-47005400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:46996000-47005200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:46998800-47005600	Weak transcription	Fetal Brain Male	brain
9	chr2:47000800-47005000	Weak transcription	HepG2	liver
10	chr2:47001000-47008600	Enhancers	Osteobl	bone
11	chr2:47002600-47005400	Weak transcription	Right Ventricle	heart
12	chr2:47002800-47005400	Weak transcription	NHLF	lung
13	chr2:47002800-47005600	Weak transcription	Right Atrium	heart
14	chr2:47002800-47007000	Weak transcription	Ovary	ovary
15	chr2:47003200-47005400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:47003200-47005800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:47004000-47005400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:47004000-47005600	Weak transcription	NHDF-Ad	bronchial
19	chr2:47004000-47006200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:47004000-47006600	Weak transcription	Colon Smooth Muscle	Colon
21	chr2:47004400-47005800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr2:47004400-47005800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:47004600-47005000	Weak transcription	A549	lung

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