Variant report

Variant	rs3803188
Chromosome Location	chr13:48808132-48808133
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 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	chr13:48806544..48809798-chr13:48876519..48878974,4	K562	blood:
5	chr13:48801755..48804565-chr13:48807877..48810629,2	K562	blood:
6	chr13:48667088..48669248-chr13:48807095..48809011,2	K562	blood:
7	chr13:48807403..48809674-chr13:48828409..48830579,2	K562	blood:
8	chr13:48806625..48809806-chr13:48877426..48879405,3	K562	blood:
9	chr13:48575152..48576683-chr13:48807803..48809574,2	K562	blood:
10	chr13:48807837..48812135-chr13:48876736..48879539,4	MCF-7	breast:
11	chr13:48667865..48670263-chr13:48806295..48809101,2	MCF-7	breast:
12	chr13:48668651..48670754-chr13:48805441..48808765,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000233610	Chromatin interaction
ENSG00000227848	Chromatin interaction
ENSG00000136143	Chromatin interaction
ENSG00000136146	Chromatin interaction
ENSG00000139687	Chromatin interaction
ENSG00000231473	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10219833	0.84[EUR][1000 genomes]
rs12100135	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12430215	0.86[CEU][hapmap]
rs12583516	0.82[ASN][1000 genomes]
rs12871662	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12871740	0.89[EUR][1000 genomes]
rs12875750	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1573601	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1886795	0.87[EUR][1000 genomes]
rs1894255	0.80[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap]
rs1925744	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1925745	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1981434	0.95[CEU][hapmap]
rs198604	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs198607	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs198612	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs198619	0.95[CEU][hapmap]
rs198634	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2243461	0.88[EUR][1000 genomes]
rs2243626	0.90[CEU][hapmap];0.89[EUR][1000 genomes]
rs2248488	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs2251813	0.88[EUR][1000 genomes]
rs2253520	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2254423	0.88[EUR][1000 genomes]
rs2406933	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2854345	0.88[ASN][1000 genomes]
rs2854355	0.82[EUR][1000 genomes]
rs34217484	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3809328	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];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs399413	0.85[CEU][hapmap]
rs4151450	0.95[CEU][hapmap]
rs4151520	0.81[ASN][1000 genomes]
rs4594153	0.86[EUR][1000 genomes]
rs4600372	0.84[EUR][1000 genomes]
rs520342	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61973349	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7358982	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7984554	0.89[EUR][1000 genomes]
rs7984795	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs7999447	0.83[EUR][1000 genomes]
rs8001315	0.89[EUR][1000 genomes]
rs9316367	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316369	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526465	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9526466	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526470	0.85[EUR][1000 genomes]
rs9526475	0.85[CEU][hapmap]
rs9534998	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535000	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535002	0.88[EUR][1000 genomes]
rs9535003	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535006	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535007	0.86[EUR][1000 genomes]
rs9535009	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535011	0.84[EUR][1000 genomes]
rs9562819	0.81[CEU][hapmap]
rs9568025	0.89[ASN][1000 genomes]
rs9568026	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568027	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568028	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9568029	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs9568032	0.89[ASN][1000 genomes]
rs9568033	0.89[ASN][1000 genomes]
rs9568034	0.89[ASN][1000 genomes]
rs9568035	0.85[CEU][hapmap];0.93[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3803188	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48806000-48808200	Active TSS	Primary hematopoietic stem cells	blood
2	chr13:48806200-48809800	Active TSS	Brain Angular Gyrus	brain
3	chr13:48806600-48808400	Active TSS	H9 Cell Line	embryonic stem cell
4	chr13:48806600-48808400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
5	chr13:48806600-48808600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:48806600-48808800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:48806600-48809200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr13:48806600-48809400	Active TSS	HSMM	muscle
9	chr13:48806600-48809800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr13:48806600-48809800	Active TSS	H1 Cell Line	embryonic stem cell
11	chr13:48806600-48809800	Active TSS	Brain Substantia Nigra	brain
12	chr13:48806600-48810000	Active TSS	Colonic Mucosa	Colon
13	chr13:48806600-48810000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr13:48806600-48810000	Active TSS	NHLF	lung
15	chr13:48806600-48810400	Active TSS	Aorta	Aorta
16	chr13:48806600-48811000	Active TSS	Psoas Muscle	Psoas
17	chr13:48806600-48811000	Active TSS	Right Ventricle	heart
18	chr13:48806600-48812200	Active TSS	Ovary	ovary
19	chr13:48806600-48812200	Active TSS	Right Atrium	heart
20	chr13:48806800-48808200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr13:48806800-48808200	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
22	chr13:48806800-48808400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:48806800-48808400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr13:48806800-48808400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr13:48806800-48808400	Active TSS	Esophagus	oesophagus
26	chr13:48806800-48808400	Active TSS	Gastric	stomach
27	chr13:48806800-48808400	Active TSS	Pancreas	Pancrea
28	chr13:48806800-48808400	Active TSS	Placenta Amnion	Placenta Amnion
29	chr13:48806800-48808400	Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr13:48806800-48808400	Active TSS	Small Intestine	intestine
31	chr13:48806800-48808600	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr13:48806800-48808600	Active TSS	Stomach Mucosa	stomach
33	chr13:48806800-48808800	Active TSS	Fetal Heart	heart
34	chr13:48806800-48809200	Active TSS	NH-A	brain
35	chr13:48806800-48809400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr13:48806800-48809400	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr13:48806800-48809400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr13:48806800-48809400	Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr13:48806800-48809400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
40	chr13:48806800-48809400	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr13:48806800-48809800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr13:48806800-48809800	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr13:48806800-48809800	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr13:48806800-48810000	Active TSS	Primary T killer memory cells from peripheral blood	blood
45	chr13:48806800-48810000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr13:48806800-48810000	Active TSS	Colon Smooth Muscle	Colon
47	chr13:48806800-48810200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr13:48806800-48810200	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr13:48806800-48810400	Active TSS	iPS-15b Cell Line	embryonic stem cell
50	chr13:48806800-48810400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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