Variant report

Variant	rs13127789
Chromosome Location	chr4:160260209-160260210
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:160260092-160260436	K562	blood:	n/a	n/a

Variant related genes	Relation type
RAPGEF2	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10022399	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723634	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11727094	0.87[ASW][hapmap];0.96[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13110592	0.96[CEU][hapmap]
rs13115272	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13131141	0.96[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13147632	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1969578	0.96[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2017052	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3749465	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6536412	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13127789	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL
rs13127789	RAPGEF2	cis	normal skin	skin_eQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160205800-160260600	Weak transcription	Aorta	Aorta
2	chr4:160224600-160262400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:160226000-160260800	Weak transcription	Colonic Mucosa	Colon
4	chr4:160226200-160270600	Weak transcription	Small Intestine	intestine
5	chr4:160230200-160263800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:160230200-160270800	Weak transcription	A549	lung
7	chr4:160230400-160260600	Weak transcription	HSMMtube	muscle
8	chr4:160231000-160260400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:160231000-160260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr4:160232200-160274600	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:160233800-160264000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr4:160235200-160266200	Weak transcription	Spleen	Spleen
13	chr4:160237000-160279400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:160237000-160284400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr4:160237400-160266200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:160237400-160274600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr4:160238600-160263800	Weak transcription	Fetal Stomach	stomach
18	chr4:160238600-160263800	Weak transcription	Lung	lung
19	chr4:160238600-160282200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr4:160241000-160281600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr4:160243000-160262400	Weak transcription	K562	blood
22	chr4:160244800-160260600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:160249600-160274000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr4:160250000-160283400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr4:160250000-160284400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr4:160250400-160285200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:160250800-160284600	Strong transcription	Liver	Liver
28	chr4:160251000-160262400	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr4:160252200-160262400	Weak transcription	NHDF-Ad	bronchial
30	chr4:160255800-160266200	Weak transcription	Psoas Muscle	Psoas
31	chr4:160257000-160267800	Weak transcription	Fetal Intestine Small	intestine
32	chr4:160257400-160262400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:160258000-160264200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr4:160258000-160283200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr4:160258200-160260600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr4:160258600-160260600	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr4:160258600-160276000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr4:160258800-160262600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr4:160258800-160269800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr4:160259000-160261200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr4:160259000-160261400	Strong transcription	Primary T cells from cord blood	blood
42	chr4:160259000-160279200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr4:160259000-160279200	Strong transcription	Adipose Nuclei	Adipose
44	chr4:160259000-160282800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr4:160259000-160282800	Strong transcription	Placenta	Placenta
46	chr4:160259200-160261200	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr4:160259200-160261200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr4:160259200-160267800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr4:160259200-160268200	Strong transcription	HUES64 Cell Line	embryonic stem cell
50	chr4:160259200-160269400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links