Variant report

Variant	rs11727094
Chromosome Location	chr4:160270232-160270233
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10022399	0.93[ASW][hapmap];0.92[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.93[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11723634	0.92[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13110592	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs13115272	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13127789	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]
rs13131141	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13147632	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1969578	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2017052	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3749465	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6536412	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11727094	RAPGEF2	cis	normal skin	skin_eQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160226200-160270600	Weak transcription	Small Intestine	intestine
2	chr4:160230200-160270800	Weak transcription	A549	lung
3	chr4:160232200-160274600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr4:160237000-160279400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:160237000-160284400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr4:160237400-160274600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr4:160238600-160282200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:160241000-160281600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr4:160249600-160274000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr4:160250000-160283400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr4:160250000-160284400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:160250400-160285200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr4:160250800-160284600	Strong transcription	Liver	Liver
14	chr4:160258000-160283200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr4:160258600-160276000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr4:160259000-160279200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr4:160259000-160279200	Strong transcription	Adipose Nuclei	Adipose
18	chr4:160259000-160282800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr4:160259000-160282800	Strong transcription	Placenta	Placenta
20	chr4:160259200-160272800	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr4:160259200-160279200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:160259200-160283000	Strong transcription	Cortex derived primary cultured neurospheres	brain
23	chr4:160259400-160270800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr4:160259400-160270800	Strong transcription	HSMM	muscle
25	chr4:160259400-160277600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr4:160259400-160278600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr4:160259400-160283000	Strong transcription	Fetal Intestine Large	intestine
28	chr4:160259600-160282800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
29	chr4:160260000-160282000	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr4:160260200-160276200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:160261000-160272000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr4:160261000-160279200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr4:160261200-160281600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:160262200-160276000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:160262200-160277200	Weak transcription	Hela-S3	cervix
36	chr4:160263000-160276200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr4:160263400-160270400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr4:160264400-160271800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr4:160264400-160283000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr4:160264600-160272000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr4:160264600-160273600	Weak transcription	Colonic Mucosa	Colon
42	chr4:160264600-160281000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr4:160264600-160283200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr4:160264600-160284800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr4:160265200-160271800	Weak transcription	HepG2	liver
46	chr4:160265200-160272000	Weak transcription	Dnd41	blood
47	chr4:160265200-160274600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr4:160265400-160271800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr4:160265400-160278000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr4:160265600-160273800	Weak transcription	Placenta Amnion	Placenta Amnion

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