Variant report

Variant	rs9562819
Chromosome Location	chr13:48974742-48974743
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11839271	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12100135	0.80[CEU][hapmap]
rs12430215	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12583516	0.83[EUR][1000 genomes]
rs1894255	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs1951775	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1981434	0.86[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1981435	0.80[AMR][1000 genomes]
rs198563	0.82[CEU][hapmap]
rs198584	0.80[CEU][hapmap]
rs198590	0.82[CEU][hapmap]
rs198604	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs198619	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2243626	0.81[CEU][hapmap]
rs375105	0.81[EUR][1000 genomes]
rs3803188	0.81[CEU][hapmap]
rs3809328	0.80[CEU][hapmap]
rs3825417	0.82[AMR][1000 genomes]
rs399413	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4151450	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4151520	0.81[EUR][1000 genomes]
rs471911	0.84[EUR][1000 genomes]
rs4942765	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7139578	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7984795	0.86[CEU][hapmap]
rs9316381	0.80[CEU][hapmap]
rs9316388	0.80[CEU][hapmap]
rs9316395	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9316399	0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap]
rs943278	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9526465	0.86[CEU][hapmap]
rs9526475	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526479	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9535015	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535016	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535018	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535032	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535033	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9568029	0.86[CEU][hapmap]
rs9568031	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9568035	0.85[CEU][hapmap]
rs9568042	0.91[AFR][1000 genomes]
rs9568043	0.80[EUR][1000 genomes]
rs990814	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.80[EUR][1000 genomes]

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
rs9562819	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48916800-48985400	Weak transcription	Colonic Mucosa	Colon
2	chr13:48925200-48974800	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr13:48925400-48976400	Weak transcription	Ovary	ovary
4	chr13:48934600-48984200	Weak transcription	Right Ventricle	heart
5	chr13:48943600-48984200	Weak transcription	Brain Angular Gyrus	brain
6	chr13:48944600-48983400	Weak transcription	Psoas Muscle	Psoas
7	chr13:48954800-48975000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr13:48956200-48976600	Weak transcription	Liver	Liver
9	chr13:48966400-48986000	Weak transcription	Lung	lung
10	chr13:48966800-48984200	Weak transcription	Placenta	Placenta
11	chr13:48968200-48976400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr13:48968400-48976600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr13:48968800-48974800	Weak transcription	Primary T cells from cord blood	blood
14	chr13:48968800-48976400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr13:48968800-48977800	Weak transcription	Spleen	Spleen
16	chr13:48968800-48984200	Weak transcription	Stomach Smooth Muscle	stomach
17	chr13:48969000-48984200	Weak transcription	Fetal Intestine Large	intestine
18	chr13:48969000-48984400	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr13:48969200-48975000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr13:48969200-48975000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr13:48969200-48976400	Weak transcription	Fetal Thymus	thymus
22	chr13:48969200-48976600	Weak transcription	Left Ventricle	heart
23	chr13:48969200-48976600	Weak transcription	Thymus	Thymus
24	chr13:48969200-48978000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr13:48969200-48978000	Weak transcription	Esophagus	oesophagus
26	chr13:48969200-48984200	Weak transcription	Fetal Stomach	stomach
27	chr13:48969200-48984400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr13:48970000-48974800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr13:48970200-48977600	Weak transcription	Fetal Muscle Trunk	muscle
30	chr13:48970400-48976400	Weak transcription	Fetal Muscle Leg	muscle
31	chr13:48970600-48984200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:48971200-48976800	Enhancers	HepG2	liver
33	chr13:48971600-48977400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr13:48971800-48975400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr13:48972000-48974800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr13:48972000-48975000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr13:48972000-48976000	Enhancers	NHLF	lung
38	chr13:48972000-48976200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr13:48972000-48976400	Enhancers	NHDF-Ad	bronchial
40	chr13:48972000-48977200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr13:48972000-48977400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr13:48972000-48977800	Enhancers	HMEC	breast
43	chr13:48972000-48978000	Enhancers	Osteobl	bone
44	chr13:48972000-48978800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr13:48972000-48980000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr13:48972200-48975000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr13:48972200-48975000	Enhancers	NHEK	skin
48	chr13:48972200-48975400	Enhancers	HUVEC	blood vessel
49	chr13:48972400-48975600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr13:48972400-48975800	Enhancers	Fetal Kidney	kidney

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