Variant report

Variant	rs198634
Chromosome Location	chr13:48913423-48913424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs12100135	0.84[ASN][1000 genomes]
rs12583516	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12871662	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12875750	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1573601	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1894255	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1925744	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1925745	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs198561	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs198563	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs198570	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs198590	0.85[AFR][1000 genomes]
rs198604	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs198607	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs198612	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs198619	0.83[EUR][1000 genomes]
rs2253520	0.92[ASN][1000 genomes]
rs2406933	0.93[ASN][1000 genomes]
rs2854345	0.99[ASN][1000 genomes]
rs2854355	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3020645	0.84[EUR][1000 genomes]
rs34217484	0.91[ASN][1000 genomes]
rs375105	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3803188	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3809328	0.89[ASN][1000 genomes]
rs3818455	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4151450	0.83[EUR][1000 genomes]
rs4151520	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs431406	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs471911	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs520342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61973349	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7358982	0.92[ASN][1000 genomes]
rs9316367	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9316369	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9526466	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9534998	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535000	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9535003	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9535006	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535009	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535015	0.81[EUR][1000 genomes]
rs9535016	0.84[EUR][1000 genomes]
rs9535018	0.81[EUR][1000 genomes]
rs9562815	0.82[ASN][1000 genomes]
rs9568025	0.84[ASN][1000 genomes]
rs9568026	0.94[ASN][1000 genomes]
rs9568027	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9568028	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568032	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568033	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568034	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568035	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039312	chr13:48898950-48925357	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1038705	chr13:48899219-48922327	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1042504	chr13:48911264-48925357	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs198634	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48880600-48924600	Weak transcription	Psoas Muscle	Psoas
2	chr13:48892600-48927800	Weak transcription	HUVEC	blood vessel
3	chr13:48894400-48913800	Weak transcription	HSMM	muscle
4	chr13:48894600-48919200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr13:48895200-48916800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr13:48895200-48923600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr13:48895200-48924600	Weak transcription	HSMMtube	muscle
8	chr13:48895400-48924800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr13:48895800-48919600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr13:48895800-48920400	Weak transcription	Right Ventricle	heart
11	chr13:48895800-48926600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr13:48896000-48919800	Weak transcription	Primary T cells from cord blood	blood
13	chr13:48897000-48917000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr13:48903400-48924400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr13:48908400-48922200	Weak transcription	Liver	Liver
16	chr13:48908400-48944800	Weak transcription	Small Intestine	intestine
17	chr13:48908800-48917000	Weak transcription	NHDF-Ad	bronchial
18	chr13:48908800-48919200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr13:48908800-48919600	Weak transcription	HMEC	breast
20	chr13:48908800-48927600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr13:48909000-48913600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr13:48909000-48913600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr13:48909000-48923600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr13:48909000-48924400	Weak transcription	Osteobl	bone
25	chr13:48909000-48972200	Weak transcription	NHEK	skin
26	chr13:48909200-48913800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr13:48909200-48916800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr13:48910400-48913600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr13:48911200-48913800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr13:48911600-48918000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr13:48911800-48919600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr13:48911800-48948400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr13:48912200-48968200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr13:48912400-48913800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr13:48912400-48914000	ZNF genes & repeats	Primary B cells from cord blood	blood
36	chr13:48912400-48914400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr13:48912600-48914000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr13:48912600-48914200	ZNF genes & repeats	Dnd41	blood
39	chr13:48912600-48914400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr13:48912800-48914000	ZNF genes & repeats	Fetal Thymus	thymus
41	chr13:48912800-48914400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
42	chr13:48912800-48917600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr13:48913000-48913600	ZNF genes & repeats	Esophagus	oesophagus
44	chr13:48913000-48913600	Strong transcription	Fetal Intestine Large	intestine
45	chr13:48913000-48913600	Strong transcription	Fetal Lung	lung
46	chr13:48913000-48913600	ZNF genes & repeats	Left Ventricle	heart
47	chr13:48913000-48913800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr13:48913000-48913800	Strong transcription	Gastric	stomach
49	chr13:48913000-48913800	ZNF genes & repeats	Thymus	Thymus
50	chr13:48913000-48914000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

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