Variant report

Variant	rs13150322
Chromosome Location	chr4:160198632-160198633
allele	A/G
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];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100215	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12499444	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12507095	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13103075	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13145422	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28562885	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4295222	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6811571	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6816396	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6824247	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6824488	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6834008	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6835746	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6847780	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6848217	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6848706	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7349689	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9990664	0.91[AMR][1000 genomes];0.91[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
rs13150322	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160149400-160216800	Weak transcription	Small Intestine	intestine
2	chr4:160173200-160217400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr4:160174000-160203400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:160186800-160225400	Weak transcription	Primary B cells from cord blood	blood
5	chr4:160188200-160201800	Weak transcription	Stomach Mucosa	stomach
6	chr4:160188800-160205200	Weak transcription	Ovary	ovary
7	chr4:160189000-160199800	Weak transcription	Fetal Intestine Small	intestine
8	chr4:160189400-160201000	Weak transcription	Pancreas	Pancrea
9	chr4:160189400-160203000	Weak transcription	Psoas Muscle	Psoas
10	chr4:160189400-160235200	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr4:160190200-160205000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr4:160190400-160203600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr4:160190600-160203000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:160190600-160205000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr4:160191200-160203000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr4:160193400-160200000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:160193400-160205600	Weak transcription	Right Ventricle	heart
18	chr4:160193400-160240200	Weak transcription	Gastric	stomach
19	chr4:160194200-160210000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr4:160194400-160202800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr4:160194400-160203000	Weak transcription	HSMMtube	muscle
22	chr4:160194400-160209600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr4:160194400-160235600	Weak transcription	Fetal Stomach	stomach
24	chr4:160194400-160236600	Weak transcription	Primary T cells from cord blood	blood
25	chr4:160194600-160203000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:160194600-160203200	Weak transcription	Fetal Brain Female	brain
27	chr4:160194600-160203600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr4:160194600-160205000	Weak transcription	Colon Smooth Muscle	Colon
29	chr4:160194600-160209400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:160194800-160199400	Weak transcription	Brain Anterior Caudate	brain
31	chr4:160194800-160199400	Weak transcription	HepG2	liver
32	chr4:160194800-160201200	Weak transcription	Fetal Kidney	kidney
33	chr4:160194800-160203000	Weak transcription	Hela-S3	cervix
34	chr4:160194800-160203600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr4:160195000-160199400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:160195200-160199400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr4:160195200-160200000	Weak transcription	Liver	Liver
38	chr4:160195200-160203600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:160195200-160203600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr4:160195200-160209800	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:160195200-160225600	Weak transcription	Placenta	Placenta
42	chr4:160195400-160200200	Weak transcription	Brain Hippocampus Middle	brain
43	chr4:160195400-160200400	Weak transcription	Left Ventricle	heart
44	chr4:160195400-160203000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr4:160195400-160205200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:160195800-160199400	Weak transcription	Adipose Nuclei	Adipose
47	chr4:160195800-160200400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr4:160196200-160199000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr4:160196200-160199800	Weak transcription	Fetal Intestine Large	intestine
50	chr4:160196200-160200000	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links