Variant report

Variant	rs558090
Chromosome Location	chr18:12439905-12439906
allele	C/G
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	POLR2A	chr18:12439603-12439906	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:12427958..12434396-chr18:12436312..12440619,6	K562	blood:
2	chr18:12436425..12438277-chr18:12439040..12441425,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267199	TF binding region
ENSG00000267108	Chromatin interaction
ENSG00000256786	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12185471	1.00[CHB][hapmap]
rs1573330	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1652670	0.84[AMR][1000 genomes]
rs3935	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs481103	0.87[EUR][1000 genomes]
rs485566	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs486498	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs496485	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs496491	0.88[EUR][1000 genomes]
rs499013	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs503307	1.00[CHB][hapmap]
rs504147	0.85[EUR][1000 genomes]
rs504863	0.84[EUR][1000 genomes]
rs509989	0.88[EUR][1000 genomes]
rs526691	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs527596	0.88[EUR][1000 genomes]
rs529538	0.89[ASW][hapmap];1.00[CHB][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes]
rs533792	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs552405	0.86[EUR][1000 genomes]
rs556734	1.00[CHB][hapmap]
rs562079	0.83[EUR][1000 genomes]
rs573390	1.00[CHB][hapmap]
rs62095752	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7243917	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers 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	79 gene(s)	inside rSNPs	diseases
3	nsv909400	chr18:12201374-12585545	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	esv2758471	chr18:12240681-12499525	Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
5	esv2758714	chr18:12240681-12499525	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
6	nsv576496	chr18:12247872-12490502	Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
7	nsv1060808	chr18:12302792-12514417	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	esv3380733	chr18:12436852-12441150	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs558090	VAPA	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12420600-12443600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr18:12420600-12477600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr18:12421200-12443400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr18:12421200-12447600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr18:12421200-12452800	Weak transcription	Colonic Mucosa	Colon
6	chr18:12421400-12444200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr18:12421800-12442400	Weak transcription	GM12878-XiMat	blood
8	chr18:12428200-12440200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr18:12428200-12440600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr18:12428400-12443400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr18:12428600-12443800	Weak transcription	HSMMtube	muscle
12	chr18:12430800-12443400	Weak transcription	A549	lung
13	chr18:12431000-12443400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr18:12431000-12443600	Weak transcription	Fetal Heart	heart
15	chr18:12431000-12447600	Weak transcription	NH-A	brain
16	chr18:12431000-12449200	Weak transcription	Pancreas	Pancrea
17	chr18:12431200-12443400	Weak transcription	Fetal Kidney	kidney
18	chr18:12431200-12447800	Weak transcription	NHEK	skin
19	chr18:12431400-12443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr18:12432000-12443800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr18:12432600-12447000	Weak transcription	HMEC	breast
22	chr18:12433000-12441400	Weak transcription	Brain Substantia Nigra	brain
23	chr18:12433000-12441600	Weak transcription	NHDF-Ad	bronchial
24	chr18:12433000-12442800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr18:12433000-12443200	Weak transcription	Primary hematopoietic stem cells	blood
26	chr18:12433000-12443600	Weak transcription	Fetal Brain Male	brain
27	chr18:12433000-12448800	Weak transcription	HUVEC	blood vessel
28	chr18:12433200-12441400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr18:12433200-12443400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr18:12433200-12443400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr18:12433200-12443600	Weak transcription	Brain Angular Gyrus	brain
32	chr18:12433200-12444000	Weak transcription	Left Ventricle	heart
33	chr18:12433200-12444000	Weak transcription	Right Ventricle	heart
34	chr18:12433200-12449200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr18:12433200-12449200	Weak transcription	Gastric	stomach
36	chr18:12433200-12449200	Weak transcription	Spleen	Spleen
37	chr18:12433200-12450200	Weak transcription	Thymus	Thymus
38	chr18:12433200-12464600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr18:12433400-12443600	Weak transcription	Brain Cingulate Gyrus	brain
40	chr18:12433400-12458600	Weak transcription	HepG2	liver
41	chr18:12434200-12443600	Weak transcription	Fetal Intestine Large	intestine
42	chr18:12434200-12477000	Weak transcription	Esophagus	oesophagus
43	chr18:12434400-12441400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr18:12434600-12443400	Weak transcription	Ovary	ovary
45	chr18:12434800-12441400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr18:12434800-12443000	Weak transcription	Fetal Lung	lung
47	chr18:12434800-12443400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr18:12435000-12441400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr18:12435000-12441400	Weak transcription	Fetal Muscle Leg	muscle
50	chr18:12435000-12441600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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