Variant report

Variant	rs198612
Chromosome Location	chr13:48976855-48976856
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11839271	0.85[EUR][1000 genomes]
rs12100135	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12583516	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12875750	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1573601	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1894255	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1951775	0.85[CEU][hapmap]
rs1981434	0.82[CEU][hapmap]
rs198561	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198563	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs198570	0.82[ASN][1000 genomes]
rs198584	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198590	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs198604	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198607	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198619	0.82[CEU][hapmap]
rs198634	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2248488	0.82[CEU][hapmap]
rs2854345	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3020645	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3092904	0.90[AFR][1000 genomes]
rs375105	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3803188	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs3809328	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3818455	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4151450	0.81[CEU][hapmap]
rs4151520	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4151635	1.00[YRI][hapmap]
rs431406	0.81[EUR][1000 genomes]
rs471911	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520342	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7139578	0.86[CEU][hapmap]
rs7984795	0.82[CEU][hapmap]
rs9316367	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs9316369	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9316381	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9316388	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9316393	0.84[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap]
rs9316395	0.86[CEU][hapmap]
rs9316399	0.86[CEU][hapmap]
rs9331991	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs9332032	1.00[YRI][hapmap]
rs943278	0.86[CEU][hapmap]
rs9526465	0.82[CEU][hapmap]
rs9534998	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9535006	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9535009	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9535032	0.86[CEU][hapmap]
rs9568029	0.82[CEU][hapmap]
rs9568032	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9568033	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9568034	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9568035	1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs990814	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1803998	chr13:48966078-48986320	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1050786	chr13:48971510-48987032	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1053432	chr13:48971510-48992810	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1043486	chr13:48971510-48996995	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs198612	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48916800-48985400	Weak transcription	Colonic Mucosa	Colon
2	chr13:48934600-48984200	Weak transcription	Right Ventricle	heart
3	chr13:48943600-48984200	Weak transcription	Brain Angular Gyrus	brain
4	chr13:48944600-48983400	Weak transcription	Psoas Muscle	Psoas
5	chr13:48966400-48986000	Weak transcription	Lung	lung
6	chr13:48966800-48984200	Weak transcription	Placenta	Placenta
7	chr13:48968800-48977800	Weak transcription	Spleen	Spleen
8	chr13:48968800-48984200	Weak transcription	Stomach Smooth Muscle	stomach
9	chr13:48969000-48984200	Weak transcription	Fetal Intestine Large	intestine
10	chr13:48969000-48984400	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr13:48969200-48978000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr13:48969200-48978000	Weak transcription	Esophagus	oesophagus
13	chr13:48969200-48984200	Weak transcription	Fetal Stomach	stomach
14	chr13:48969200-48984400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:48970200-48977600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr13:48970600-48984200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:48971600-48977400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr13:48972000-48977200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr13:48972000-48977400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr13:48972000-48977800	Enhancers	HMEC	breast
21	chr13:48972000-48978000	Enhancers	Osteobl	bone
22	chr13:48972000-48978800	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr13:48972000-48980000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr13:48972600-48982600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr13:48972800-48977600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr13:48973600-48977200	Enhancers	Adipose Nuclei	Adipose
27	chr13:48973800-48978600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr13:48973800-48984000	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr13:48974000-48977200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr13:48974000-48977200	Enhancers	Fetal Lung	lung
31	chr13:48974400-48979000	Enhancers	Primary hematopoietic stem cells	blood
32	chr13:48974600-48977200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr13:48974600-48977600	Enhancers	Muscle Satellite Cultured Cells	--
34	chr13:48974600-48977600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr13:48974600-48978400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr13:48974600-48986000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr13:48974800-48978000	Enhancers	Primary T cells from cord blood	blood
38	chr13:48975000-48977400	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr13:48975200-48977000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr13:48975200-48977200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr13:48975200-48978000	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr13:48975200-48978200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr13:48975200-48978600	Weak transcription	Colon Smooth Muscle	Colon
44	chr13:48975200-48979800	Weak transcription	Fetal Heart	heart
45	chr13:48975200-48980600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr13:48975200-48983800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr13:48975200-48984000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr13:48975200-48984200	Weak transcription	Fetal Intestine Small	intestine
49	chr13:48975200-48985400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr13:48975400-48977200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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