Variant report

Variant	rs7989287
Chromosome Location	chr13:49228965-49228966
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1009717	0.89[ASN][1000 genomes]
rs1009718	0.89[ASN][1000 genomes]
rs11840006	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12867213	0.90[ASN][1000 genomes]
rs12874937	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1323556	0.81[ASN][1000 genomes]
rs1359108	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1359109	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1575464	0.81[ASN][1000 genomes]
rs1575465	0.81[ASN][1000 genomes]
rs1575920	0.89[ASN][1000 genomes]
rs1854017	0.89[ASN][1000 genomes]
rs1980838	0.85[EUR][1000 genomes]
rs1980839	0.85[EUR][1000 genomes]
rs2146861	0.85[EUR][1000 genomes]
rs2406937	0.89[ASN][1000 genomes]
rs2406938	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2406939	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2407246	0.81[ASN][1000 genomes]
rs2897623	0.81[ASN][1000 genomes]
rs4451857	0.89[ASN][1000 genomes]
rs4942769	0.83[ASN][1000 genomes]
rs6561469	0.89[ASN][1000 genomes]
rs6561474	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7323160	0.81[ASN][1000 genomes]
rs7324562	0.88[ASN][1000 genomes]
rs7990619	0.89[ASN][1000 genomes]
rs7990660	0.89[ASN][1000 genomes]
rs8001736	0.90[ASN][1000 genomes]
rs8002035	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9535060	0.90[ASN][1000 genomes]
rs9562833	0.89[ASN][1000 genomes]
rs9562835	0.81[EUR][1000 genomes]
rs9562836	0.81[EUR][1000 genomes]
rs9568056	0.89[ASN][1000 genomes]
rs9568058	0.89[ASN][1000 genomes]
rs9568061	0.88[ASN][1000 genomes]
rs9568062	0.89[ASN][1000 genomes]
rs9568064	0.90[ASN][1000 genomes]
rs9568065	0.90[ASN][1000 genomes]
rs9568077	0.81[EUR][1000 genomes]
rs9591187	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9595943	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9595944	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9595950	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs964413	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7989287	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49222600-49229400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:49227000-49229000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr13:49227000-49229000	Enhancers	Fetal Lung	lung
4	chr13:49227200-49230000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr13:49227400-49230000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr13:49227600-49229400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr13:49227600-49229800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr13:49227600-49229800	Active TSS	Brain Anterior Caudate	brain
9	chr13:49227600-49230400	Weak transcription	Fetal Intestine Large	intestine
10	chr13:49227800-49229000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
11	chr13:49227800-49229000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr13:49227800-49229400	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr13:49227800-49229400	Active TSS	Right Atrium	heart
14	chr13:49228000-49230000	Active TSS	Left Ventricle	heart
15	chr13:49228000-49230000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr13:49228000-49230400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr13:49228000-49230400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr13:49228000-49230800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr13:49228200-49229000	Enhancers	Fetal Brain Male	brain
20	chr13:49228200-49229400	Weak transcription	Gastric	stomach
21	chr13:49228200-49229400	Weak transcription	Small Intestine	intestine
22	chr13:49228200-49229800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr13:49228200-49230400	Weak transcription	Fetal Intestine Small	intestine
24	chr13:49228200-49230600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr13:49228200-49230600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr13:49228200-49230600	Weak transcription	Brain Hippocampus Middle	brain
27	chr13:49228200-49231400	Weak transcription	Placenta	Placenta
28	chr13:49228200-49234200	Weak transcription	GM12878-XiMat	blood
29	chr13:49228400-49229400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr13:49228400-49230000	Enhancers	Primary hematopoietic stem cells	blood
31	chr13:49228400-49230600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr13:49228600-49229000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
33	chr13:49228600-49229000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr13:49228600-49229000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr13:49228600-49229000	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr13:49228600-49229200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr13:49228600-49230400	Weak transcription	Thymus	Thymus
38	chr13:49228600-49231400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr13:49228800-49229000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr13:49228800-49229000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr13:49228800-49229600	Enhancers	Primary T cells from cord blood	blood
42	chr13:49228800-49229600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr13:49228800-49229800	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr13:49228800-49231200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr13:49228800-49231400	Flanking Active TSS	Dnd41	blood

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