Variant report

Variant	rs13103075
Chromosome Location	chr4:160225430-160225431
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10017696	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11100215	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12499444	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12507095	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145422	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13150322	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28562885	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4295222	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6811571	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6816396	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6824247	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6824488	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6834008	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6835746	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847780	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6848217	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6848706	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7349689	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990664	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830129	chr4:160061694-160270760	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	nsv1022771	chr4:160188801-160324683	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13103075	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160189400-160235200	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr4:160193400-160240200	Weak transcription	Gastric	stomach
3	chr4:160194400-160235600	Weak transcription	Fetal Stomach	stomach
4	chr4:160194400-160236600	Weak transcription	Primary T cells from cord blood	blood
5	chr4:160195200-160225600	Weak transcription	Placenta	Placenta
6	chr4:160200600-160235600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr4:160205800-160236400	Weak transcription	Pancreas	Pancrea
8	chr4:160205800-160260600	Weak transcription	Aorta	Aorta
9	chr4:160206200-160229000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr4:160210000-160229200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr4:160210600-160238000	Weak transcription	Adipose Nuclei	Adipose
12	chr4:160210800-160226000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr4:160215200-160236800	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr4:160215400-160225600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr4:160215600-160225800	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr4:160216200-160225800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr4:160216600-160237600	Weak transcription	Stomach Smooth Muscle	stomach
18	chr4:160217000-160225800	Weak transcription	Left Ventricle	heart
19	chr4:160217000-160226000	Weak transcription	Small Intestine	intestine
20	chr4:160217000-160259400	Weak transcription	Fetal Brain Male	brain
21	chr4:160217400-160229200	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr4:160218200-160229000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr4:160218400-160229200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr4:160218400-160232400	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:160218600-160226400	Weak transcription	Fetal Heart	heart
26	chr4:160218600-160232400	Weak transcription	Psoas Muscle	Psoas
27	chr4:160219800-160226600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr4:160220000-160225600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:160220000-160225800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:160220000-160225800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:160220000-160225800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr4:160220000-160225800	Weak transcription	Fetal Lung	lung
33	chr4:160220000-160232400	Weak transcription	Right Ventricle	heart
34	chr4:160220000-160232600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:160220000-160244400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr4:160220200-160225800	Weak transcription	HUVEC	blood vessel
37	chr4:160220400-160225800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr4:160220400-160226000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:160220400-160229000	Weak transcription	NHDF-Ad	bronchial
40	chr4:160220400-160229000	Weak transcription	NHLF	lung
41	chr4:160220400-160229000	Weak transcription	Osteobl	bone
42	chr4:160220400-160229200	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:160220400-160229200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr4:160220400-160229600	Weak transcription	HSMMtube	muscle
45	chr4:160220600-160225800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:160220600-160225800	Weak transcription	Brain Angular Gyrus	brain
47	chr4:160220600-160229000	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr4:160220600-160229600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr4:160220800-160225600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr4:160220800-160225800	Weak transcription	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links