Variant report

Variant	rs3809328
Chromosome Location	chr13:48806510-48806511
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr13:48806307-48806604	HepG2	liver:	n/a	n/a
2	FOXA1	chr13:48806172-48806687	HepG2	liver:	n/a	n/a
3	MXI1	chr13:48806484-48808649	SK-N-SH	brain:	n/a	n/a
4	FOXA1	chr13:48806220-48806759	HepG2	liver:	n/a	n/a
5	MXI1	chr13:48806509-48808033	HepG2	liver:	n/a	n/a
6	POLR2A	chr13:48806291-48808234	HepG2	liver:	n/a	n/a
7	POLR2A	chr13:48806283-48806525	HepG2	liver:	n/a	n/a
8	RCOR1	chr13:48806486-48807904	HepG2	liver:	n/a	n/a
9	FOXA1	chr13:48806231-48806735	HepG2	liver:	n/a	n/a
10	FOXA2	chr13:48806317-48806574	HepG2	liver:	n/a	n/a
11	HEY1	chr13:48806258-48808020	HepG2	liver:	n/a	chr13:48807707-48807722 chr13:48807698-48807713

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:48806118..48810225-chr13:48876144..48879386,12	MCF-7	breast:
2	chr13:48806307..48808548-chr13:49152200..49154470,2	MCF-7	breast:
3	chr13:48612019..48613651-chr13:48806032..48808331,2	MCF-7	breast:
4	chr13:48805537..48807049-chr13:48830310..48832562,2	K562	blood:
5	chr13:48667865..48670263-chr13:48806295..48809101,2	MCF-7	breast:
6	chr13:48668651..48670754-chr13:48805441..48808765,3	MCF-7	breast:

No data

Variant related genes	Relation type
ITM2B	TF binding region
ENSG00000136146	Chromatin interaction
ENSG00000136143	Chromatin interaction
ENSG00000233610	Chromatin interaction
ENSG00000231473	Chromatin interaction
ENSG00000139687	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10219833	0.89[EUR][1000 genomes]
rs12100135	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];1.00[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];0.93[ASN][1000 genomes]
rs12430215	0.85[CEU][hapmap]
rs12583516	0.82[ASN][1000 genomes]
rs12871662	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12871740	0.94[EUR][1000 genomes]
rs12875750	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1573601	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1886795	0.91[EUR][1000 genomes]
rs1894255	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap]
rs1925744	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1925745	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1981434	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs198604	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs198607	0.90[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs198612	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198619	0.95[CEU][hapmap]
rs198634	0.89[ASN][1000 genomes]
rs2243461	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2243626	0.90[CEU][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs2248488	0.85[CEU][hapmap];0.95[EUR][1000 genomes]
rs2251813	0.93[EUR][1000 genomes]
rs2253520	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2254423	0.93[EUR][1000 genomes]
rs2406933	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2854345	0.88[ASN][1000 genomes]
rs34217484	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3803188	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3818455	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs399413	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs4151450	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs4151520	0.81[ASN][1000 genomes]
rs4594153	0.91[EUR][1000 genomes]
rs4600372	0.88[EUR][1000 genomes]
rs520342	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs61973349	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7322987	0.86[EUR][1000 genomes]
rs7337883	0.80[EUR][1000 genomes]
rs7358982	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7984554	0.94[EUR][1000 genomes]
rs7984795	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs7999447	0.89[EUR][1000 genomes]
rs8001315	0.94[EUR][1000 genomes]
rs9316367	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9316369	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526465	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs9526466	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526470	0.84[EUR][1000 genomes]
rs9526475	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs9534996	0.87[EUR][1000 genomes]
rs9534998	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535000	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535002	0.93[EUR][1000 genomes]
rs9535003	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535006	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535007	0.91[EUR][1000 genomes]
rs9535009	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535011	0.89[EUR][1000 genomes]
rs9562819	0.80[CEU][hapmap]
rs9568025	0.93[ASN][1000 genomes]
rs9568026	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9568027	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9568028	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9568029	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs9568032	0.89[ASN][1000 genomes]
rs9568033	0.89[ASN][1000 genomes]
rs9568034	0.89[ASN][1000 genomes]
rs9568035	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[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	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1043294	chr13:48762477-48810028	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3809328	LPAR6	cis	parietal	SCAN
rs3809328	ATAD2	trans	parietal	SCAN
rs3809328	ITM2B	cis	lymphoblastoid	seeQTL
rs3809328	DLEU1	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48796000-48806800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr13:48804200-48806600	Enhancers	Fetal Intestine Large	intestine
3	chr13:48804400-48806600	Enhancers	Fetal Intestine Small	intestine
4	chr13:48804600-48806800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr13:48804800-48806600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr13:48804800-48806800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr13:48805000-48806800	Flanking Active TSS	HepG2	liver
8	chr13:48805200-48806600	Enhancers	Fetal Lung	lung
9	chr13:48805400-48806600	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr13:48805400-48806800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr13:48805800-48806600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr13:48805800-48806600	Enhancers	Brain Germinal Matrix	brain
13	chr13:48805800-48806600	Enhancers	Colon Smooth Muscle	Colon
14	chr13:48805800-48806600	Enhancers	Fetal Stomach	stomach
15	chr13:48805800-48806800	Weak transcription	Hela-S3	cervix
16	chr13:48806000-48806600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr13:48806000-48806600	Enhancers	Brain Cingulate Gyrus	brain
18	chr13:48806000-48806600	Enhancers	Small Intestine	intestine
19	chr13:48806000-48806800	Enhancers	Placenta	Placenta
20	chr13:48806000-48806800	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr13:48806000-48807000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr13:48806000-48808200	Active TSS	Primary hematopoietic stem cells	blood
23	chr13:48806200-48806600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
24	chr13:48806200-48806600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr13:48806200-48806600	Enhancers	Primary B cells from peripheral blood	blood
26	chr13:48806200-48806600	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr13:48806200-48806600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr13:48806200-48806600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr13:48806200-48806600	Enhancers	Aorta	Aorta
30	chr13:48806200-48806600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr13:48806200-48806600	Enhancers	Fetal Muscle Leg	muscle
32	chr13:48806200-48806600	Enhancers	Fetal Thymus	thymus
33	chr13:48806200-48806600	Enhancers	Left Ventricle	heart
34	chr13:48806200-48806600	Enhancers	Ovary	ovary
35	chr13:48806200-48806600	Enhancers	Right Atrium	heart
36	chr13:48806200-48806600	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr13:48806200-48806600	Active TSS	Stomach Smooth Muscle	stomach
38	chr13:48806200-48806600	Enhancers	HMEC	breast
39	chr13:48806200-48806600	Bivalent Enhancer	NHDF-Ad	bronchial
40	chr13:48806200-48806800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr13:48806200-48806800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr13:48806200-48806800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr13:48806200-48806800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr13:48806200-48806800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
45	chr13:48806200-48806800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr13:48806200-48806800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr13:48806200-48806800	Enhancers	Gastric	stomach
48	chr13:48806200-48806800	Enhancers	Lung	lung
49	chr13:48806200-48806800	Enhancers	Pancreas	Pancrea
50	chr13:48806200-48807000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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