Variant report

Variant	rs375105
Chromosome Location	chr13:48971231-48971232
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12430215	0.83[EUR][1000 genomes]
rs12583516	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12871662	0.81[EUR][1000 genomes]
rs12875750	0.81[EUR][1000 genomes]
rs1573601	0.81[EUR][1000 genomes]
rs1894255	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1925744	0.81[EUR][1000 genomes]
rs1925745	0.81[EUR][1000 genomes]
rs198561	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198563	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs198570	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs198590	0.89[AFR][1000 genomes]
rs198604	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198607	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198612	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs198634	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2854345	0.81[ASN][1000 genomes]
rs2854355	0.83[EUR][1000 genomes]
rs3020645	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3818455	0.81[EUR][1000 genomes]
rs399413	0.82[EUR][1000 genomes]
rs4151520	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs431406	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs471911	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942765	0.84[EUR][1000 genomes]
rs520342	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61973349	0.81[EUR][1000 genomes]
rs9316367	0.81[EUR][1000 genomes]
rs9316369	0.81[EUR][1000 genomes]
rs9316381	0.82[AFR][1000 genomes]
rs9526466	0.81[EUR][1000 genomes]
rs9526475	0.82[EUR][1000 genomes]
rs9534998	0.81[EUR][1000 genomes]
rs9535000	0.81[EUR][1000 genomes]
rs9535003	0.81[EUR][1000 genomes]
rs9535006	0.81[EUR][1000 genomes]
rs9535009	0.81[EUR][1000 genomes]
rs9562819	0.81[EUR][1000 genomes]
rs9568027	0.81[EUR][1000 genomes]
rs9568028	0.81[EUR][1000 genomes]
rs9568032	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568033	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568034	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9568035	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]

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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs375105	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48909000-48972200	Weak transcription	NHEK	skin
2	chr13:48914800-48972000	Weak transcription	NHLF	lung
3	chr13:48916800-48985400	Weak transcription	Colonic Mucosa	Colon
4	chr13:48920200-48974400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr13:48921600-48972000	Weak transcription	Stomach Mucosa	stomach
6	chr13:48925200-48974800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr13:48925400-48976400	Weak transcription	Ovary	ovary
8	chr13:48926800-48972000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr13:48928200-48971800	Weak transcription	A549	lung
10	chr13:48933400-48974000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr13:48934600-48984200	Weak transcription	Right Ventricle	heart
12	chr13:48936000-48974600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr13:48936400-48973200	Weak transcription	Hela-S3	cervix
14	chr13:48941800-48973200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr13:48943600-48984200	Weak transcription	Brain Angular Gyrus	brain
16	chr13:48944000-48974400	Weak transcription	Brain Anterior Caudate	brain
17	chr13:48944200-48973800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr13:48944600-48983400	Weak transcription	Psoas Muscle	Psoas
19	chr13:48945000-48972000	Weak transcription	HSMMtube	muscle
20	chr13:48945400-48974400	Weak transcription	Small Intestine	intestine
21	chr13:48949400-48972800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr13:48953800-48972000	Weak transcription	Osteobl	bone
23	chr13:48954400-48972200	Weak transcription	HUVEC	blood vessel
24	chr13:48954800-48975000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr13:48955800-48972000	Weak transcription	HMEC	breast
26	chr13:48955800-48972000	Weak transcription	NHDF-Ad	bronchial
27	chr13:48956000-48974000	Weak transcription	Colon Smooth Muscle	Colon
28	chr13:48956200-48976600	Weak transcription	Liver	Liver
29	chr13:48959800-48972200	Weak transcription	Adipose Nuclei	Adipose
30	chr13:48961000-48972000	Weak transcription	Fetal Lung	lung
31	chr13:48964000-48974400	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr13:48965200-48974400	Weak transcription	Fetal Heart	heart
33	chr13:48966000-48971800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr13:48966200-48971600	Weak transcription	Aorta	Aorta
35	chr13:48966400-48974200	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr13:48966400-48986000	Weak transcription	Lung	lung
37	chr13:48966800-48984200	Weak transcription	Placenta	Placenta
38	chr13:48967600-48974600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr13:48967800-48972000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr13:48967800-48972400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr13:48968200-48972000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr13:48968200-48972800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr13:48968200-48976400	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr13:48968400-48976600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr13:48968800-48972400	Weak transcription	Fetal Kidney	kidney
46	chr13:48968800-48974200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr13:48968800-48974800	Weak transcription	Primary T cells from cord blood	blood
48	chr13:48968800-48976400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr13:48968800-48977800	Weak transcription	Spleen	Spleen
50	chr13:48968800-48984200	Weak transcription	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links