Variant report

Variant	rs1925745
Chromosome Location	chr13:48840064-48840065
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:48839695..48841819-chr13:48848879..48850902,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10219833	0.87[EUR][1000 genomes]
rs12100135	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12583516	0.84[ASN][1000 genomes]
rs12871662	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12871740	0.86[EUR][1000 genomes]
rs12875750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1573601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1886795	0.87[EUR][1000 genomes]
rs1894255	0.83[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs1925744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1951775	0.84[CEU][hapmap]
rs1981434	0.90[CEU][hapmap]
rs198561	0.83[EUR][1000 genomes]
rs198563	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198584	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198590	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198604	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes]
rs198607	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198612	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs198619	0.90[CEU][hapmap]
rs198634	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2243461	0.86[EUR][1000 genomes]
rs2243626	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2248488	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs2251813	0.86[EUR][1000 genomes]
rs2253520	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2254423	0.86[EUR][1000 genomes]
rs2406933	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2854345	0.91[ASN][1000 genomes]
rs2854355	0.86[EUR][1000 genomes]
rs34217484	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs375105	0.81[EUR][1000 genomes]
rs3803188	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809328	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818455	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4151450	0.90[CEU][hapmap]
rs4151520	0.84[ASN][1000 genomes]
rs4594153	0.84[EUR][1000 genomes]
rs4600372	0.81[EUR][1000 genomes]
rs520342	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61973349	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7358982	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7984554	0.86[EUR][1000 genomes]
rs7984795	0.90[CEU][hapmap];0.87[EUR][1000 genomes]
rs7999447	0.87[EUR][1000 genomes]
rs8001315	0.86[EUR][1000 genomes]
rs9316367	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9316369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526465	0.90[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9526466	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9526470	0.89[EUR][1000 genomes]
rs9534998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535000	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535002	0.86[EUR][1000 genomes]
rs9535003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535007	0.84[EUR][1000 genomes]
rs9535009	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535011	0.87[EUR][1000 genomes]
rs9535032	0.85[CEU][hapmap]
rs9562815	0.86[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs9568025	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9568026	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568027	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568028	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9568029	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs9568032	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568033	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568034	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568035	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.92[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	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1925745	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48808400-48843600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr13:48810800-48841000	Weak transcription	Hela-S3	cervix
3	chr13:48811200-48843800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr13:48825400-48841200	Strong transcription	Fetal Thymus	thymus
5	chr13:48825400-48844400	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr13:48826400-48841200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr13:48826800-48842000	Weak transcription	K562	blood
8	chr13:48827400-48840200	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr13:48827600-48841000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr13:48827600-48843600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr13:48827800-48840800	Strong transcription	Placenta	Placenta
12	chr13:48827800-48843800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:48828000-48840400	Strong transcription	Duodenum Mucosa	Duodenum
14	chr13:48828600-48840200	Strong transcription	Adipose Nuclei	Adipose
15	chr13:48828600-48845800	Weak transcription	Stomach Mucosa	stomach
16	chr13:48828800-48840800	Strong transcription	Liver	Liver
17	chr13:48829800-48843400	Weak transcription	Spleen	Spleen
18	chr13:48830800-48840800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr13:48831200-48841200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr13:48832800-48845200	Weak transcription	Fetal Intestine Small	intestine
21	chr13:48833000-48843200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr13:48833400-48840400	Strong transcription	Fetal Kidney	kidney
23	chr13:48833400-48840600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr13:48833600-48840400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr13:48833600-48843600	Weak transcription	Pancreas	Pancrea
26	chr13:48833600-48844400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr13:48833800-48851600	Weak transcription	Fetal Heart	heart
28	chr13:48835800-48849400	Weak transcription	NHLF	lung
29	chr13:48836400-48840400	Strong transcription	Stomach Smooth Muscle	stomach
30	chr13:48836400-48840600	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr13:48836800-48840400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr13:48837200-48840600	Strong transcription	Fetal Stomach	stomach
33	chr13:48837200-48841200	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr13:48837400-48841400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr13:48837800-48841000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr13:48837800-48848000	Weak transcription	A549	lung
37	chr13:48837800-48848600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:48837800-48848600	Weak transcription	Fetal Brain Female	brain
39	chr13:48837800-48853000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr13:48837800-48856400	Weak transcription	Colon Smooth Muscle	Colon
41	chr13:48838000-48840600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr13:48838000-48840800	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr13:48838000-48841000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr13:48838000-48841000	Weak transcription	NHEK	skin
45	chr13:48838000-48841200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr13:48838000-48841200	Weak transcription	Fetal Brain Male	brain
47	chr13:48838000-48841200	Weak transcription	Small Intestine	intestine
48	chr13:48838000-48841400	Enhancers	Primary B cells from peripheral blood	blood
49	chr13:48838000-48842600	Weak transcription	Thymus	Thymus
50	chr13:48838000-48843000	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links