Variant report

Variant	rs11723634
Chromosome Location	chr4:160267334-160267335
allele	C/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	chr4:160266198-160267549	K562	blood:	n/a	n/a

Variant related genes	Relation type
RAPGEF2	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10021753	0.82[YRI][hapmap]
rs10022399	0.92[CEU][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11100215	0.83[GIH][hapmap]
rs11727094	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	0.96[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13115272	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13127789	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]
rs13131141	0.92[CEU][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13147632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1969578	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2017052	0.83[EUR][1000 genomes]
rs3749465	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4295222	0.83[GIH][hapmap]
rs6536412	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6811571	0.83[GIH][hapmap]
rs6816396	0.80[GIH][hapmap];1.00[YRI][hapmap]
rs6824247	1.00[YRI][hapmap]
rs6835746	1.00[YRI][hapmap]

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
rs11723634	RAPGEF2	cis	normal skin	skin_eQTL

Chromatin state (count:125 , 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	chr4:160257000-160267800	Weak transcription	Fetal Intestine Small	intestine
15	chr4:160258000-160283200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr4:160258600-160276000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr4:160258800-160269800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr4:160259000-160279200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:160259000-160279200	Strong transcription	Adipose Nuclei	Adipose
20	chr4:160259000-160282800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:160259000-160282800	Strong transcription	Placenta	Placenta
22	chr4:160259200-160267800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:160259200-160268200	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:160259200-160269400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:160259200-160272800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr4:160259200-160279200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:160259200-160283000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr4:160259400-160268400	Strong transcription	Primary hematopoietic stem cells	blood
29	chr4:160259400-160268600	Strong transcription	Duodenum Mucosa	Duodenum
30	chr4:160259400-160270000	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr4:160259400-160270000	Strong transcription	Stomach Smooth Muscle	stomach
32	chr4:160259400-160270200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr4:160259400-160270800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr4:160259400-160270800	Strong transcription	HSMM	muscle
35	chr4:160259400-160277600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:160259400-160278600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:160259400-160283000	Strong transcription	Fetal Intestine Large	intestine
38	chr4:160259600-160268200	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:160259600-160282800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr4:160260000-160282000	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr4:160260200-160276200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:160260400-160268400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr4:160261000-160272000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr4:160261000-160279200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr4:160261200-160281600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr4:160262000-160269600	Strong transcription	Brain Angular Gyrus	brain
47	chr4:160262200-160268200	Strong transcription	Primary T cells from cord blood	blood
48	chr4:160262200-160268400	Strong transcription	NH-A	brain
49	chr4:160262200-160269800	Strong transcription	Brain Anterior Caudate	brain
50	chr4:160262200-160276000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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