Variant report

Variant	rs198563
Chromosome Location	chr13:49010485-49010486
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12583516	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12875750	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1573601	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1894255	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1951775	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs1981434	0.86[CEU][hapmap]
rs198561	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs198570	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs198590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs198604	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs198607	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs198612	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs198619	0.86[CEU][hapmap]
rs198634	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2243626	0.81[CEU][hapmap]
rs2248488	0.86[CEU][hapmap]
rs2854355	0.85[AFR][1000 genomes]
rs3020645	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3092904	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs375105	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3818455	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4151450	0.85[CEU][hapmap]
rs4151520	0.82[EUR][1000 genomes]
rs431406	0.89[AFR][1000 genomes]
rs471911	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs520342	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7139578	0.90[CEU][hapmap]
rs7984795	0.86[CEU][hapmap]
rs9316367	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs9316369	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9316381	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9316388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9316393	0.89[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs9316395	0.90[CEU][hapmap]
rs9316399	0.91[CEU][hapmap]
rs9331991	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs943278	0.91[CEU][hapmap]
rs9526465	0.86[CEU][hapmap]
rs9534998	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9535006	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9535009	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs9535032	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs9535033	0.85[EUR][1000 genomes]
rs9535038	0.80[EUR][1000 genomes]
rs9562819	0.82[CEU][hapmap]
rs9568029	0.86[CEU][hapmap]
rs9568032	0.98[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9568033	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9568034	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9568035	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9568047	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs990814	0.90[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs198563	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48990800-49011600	Weak transcription	Left Ventricle	heart
2	chr13:48990800-49030800	Weak transcription	Ovary	ovary
3	chr13:48991400-49013200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr13:48991400-49018600	Weak transcription	Thymus	Thymus
5	chr13:48991400-49019200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:48991400-49030600	Weak transcription	Spleen	Spleen
7	chr13:48991600-49010800	Weak transcription	Fetal Stomach	stomach
8	chr13:48991800-49018800	Weak transcription	Fetal Thymus	thymus
9	chr13:48994800-49018000	Weak transcription	Primary B cells from cord blood	blood
10	chr13:48997800-49011200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr13:48999000-49024400	Weak transcription	Fetal Muscle Leg	muscle
12	chr13:49001400-49010600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:49001400-49022400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr13:49001400-49024600	Weak transcription	Fetal Intestine Small	intestine
15	chr13:49003000-49012600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr13:49003600-49011600	Weak transcription	Pancreas	Pancrea
17	chr13:49003600-49023200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr13:49006000-49018000	Weak transcription	Dnd41	blood
19	chr13:49006400-49018800	Weak transcription	GM12878-XiMat	blood
20	chr13:49006600-49010800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr13:49006600-49011400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr13:49006600-49011600	Weak transcription	Brain Anterior Caudate	brain
23	chr13:49006800-49010600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr13:49006800-49010600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:49006800-49010600	Weak transcription	HMEC	breast
26	chr13:49006800-49010800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr13:49006800-49010800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr13:49006800-49010800	Weak transcription	NHDF-Ad	bronchial
29	chr13:49006800-49010800	Weak transcription	NHLF	lung
30	chr13:49006800-49011000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr13:49006800-49011000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr13:49006800-49011000	Weak transcription	Colon Smooth Muscle	Colon
33	chr13:49006800-49011200	Weak transcription	HSMM	muscle
34	chr13:49006800-49011600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr13:49006800-49020200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr13:49006800-49020400	Weak transcription	HSMMtube	muscle
37	chr13:49006800-49020800	Weak transcription	Hela-S3	cervix
38	chr13:49006800-49030400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr13:49007000-49011000	Weak transcription	Osteobl	bone
40	chr13:49007000-49011200	Weak transcription	Fetal Kidney	kidney
41	chr13:49007000-49027600	Weak transcription	Primary T cells from cord blood	blood
42	chr13:49007200-49010600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:49007200-49010800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr13:49007200-49010800	Weak transcription	Fetal Lung	lung
45	chr13:49007200-49011000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr13:49007200-49011000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr13:49007800-49010600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr13:49008000-49010600	Weak transcription	Primary hematopoietic stem cells	blood
49	chr13:49008000-49028600	Weak transcription	HepG2	liver
50	chr13:49008400-49010800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links