Variant report

Variant	rs2785730
Chromosome Location	chr9:1707568-1707569
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10738438	0.88[EUR][1000 genomes]
rs2093648	0.80[EUR][1000 genomes]
rs2760394	0.87[EUR][1000 genomes]
rs2760395	0.88[EUR][1000 genomes]
rs2760397	0.88[EUR][1000 genomes]
rs2760398	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2783994	0.87[EUR][1000 genomes]
rs4741574	0.85[EUR][1000 genomes]
rs652703	0.81[EUR][1000 genomes]
rs808853	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9298765	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752273	chr9:1062218-1824888	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1026043	chr9:1079462-1732502	Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv539909	chr9:1079462-1732502	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1031422	chr9:1318383-1716944	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv539912	chr9:1318383-1716944	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1032384	chr9:1320386-1719409	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv539913	chr9:1320386-1719409	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	nsv892035	chr9:1556054-1823605	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv1016764	chr9:1564704-1736070	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv1021954	chr9:1591579-1722416	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv1021712	chr9:1647840-2216839	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv539921	chr9:1647840-2216839	Bivalent Enhancer Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv892039	chr9:1663954-1715256	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv892040	chr9:1672167-1759486	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	nsv892041	chr9:1690810-1759486	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
18	nsv613076	chr9:1699307-1747566	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	nsv1018906	chr9:1702711-1743631	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	nsv539922	chr9:1702711-1743631	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
21	nsv522744	chr9:1707518-1707568	Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2785730	VLDLR	cis	parietal	SCAN
rs2785730	VPS39	trans	lymphoblastoid	seeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:1707200-1707800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr9:1707200-1707800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr9:1707200-1707800	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr9:1707200-1707800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:1707200-1708000	Enhancers	NHEK	skin
6	chr9:1707200-1708600	Enhancers	HMEC	breast
7	chr9:1707400-1707800	Enhancers	HUES64 Cell Line	embryonic stem cell

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