Variant report

Variant	rs10022399
Chromosome Location	chr4:160249722-160249723
allele	A/G
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	STAT3	chr4:160249641-160249838	MCF10A-Er-Src	breast:	n/a	n/a
2	MAFK	chr4:160249613-160249831	K562	blood:	n/a	n/a
3	EP300	chr4:160249662-160250313	K562	blood:	n/a	n/a

Variant related genes	Relation type
RAPGEF2	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11100215	0.80[GIH][hapmap]
rs11723634	0.92[CEU][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11727094	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]
rs13110592	0.92[CEU][hapmap]
rs13115272	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13127789	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]
rs13131141	0.92[CEU][hapmap];0.88[GIH][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13147632	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1969578	0.92[CEU][hapmap];0.88[GIH][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs2017052	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3749465	0.96[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4295222	0.80[GIH][hapmap]
rs6536412	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6811571	0.80[GIH][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
rs10022399	RAPGEF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160205800-160260600	Weak transcription	Aorta	Aorta
2	chr4:160217000-160259400	Weak transcription	Fetal Brain Male	brain
3	chr4:160223000-160260000	Weak transcription	Ovary	ovary
4	chr4:160224600-160262400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr4:160225200-160260200	Weak transcription	Thymus	Thymus
6	chr4:160225600-160253600	Weak transcription	HepG2	liver
7	chr4:160226000-160260800	Weak transcription	Colonic Mucosa	Colon
8	chr4:160226200-160270600	Weak transcription	Small Intestine	intestine
9	chr4:160230000-160251800	Weak transcription	NHDF-Ad	bronchial
10	chr4:160230200-160263800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr4:160230200-160270800	Weak transcription	A549	lung
12	chr4:160230400-160253600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr4:160230400-160259400	Weak transcription	NHLF	lung
14	chr4:160230400-160260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:160230400-160260600	Weak transcription	HSMMtube	muscle
16	chr4:160230600-160260000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr4:160231000-160259400	Weak transcription	HMEC	breast
18	chr4:160231000-160260400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:160231000-160260400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:160232200-160274600	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr4:160232800-160253400	Weak transcription	Psoas Muscle	Psoas
22	chr4:160233000-160253400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:160233000-160260000	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:160233600-160259600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr4:160233800-160264000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr4:160234000-160259400	Weak transcription	Esophagus	oesophagus
27	chr4:160234200-160260200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:160235200-160266200	Weak transcription	Spleen	Spleen
29	chr4:160236000-160252600	Weak transcription	Osteobl	bone
30	chr4:160236000-160259400	Weak transcription	Brain Angular Gyrus	brain
31	chr4:160236800-160260200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr4:160237000-160279400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:160237000-160284400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:160237200-160252600	Weak transcription	Brain Substantia Nigra	brain
35	chr4:160237200-160254200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr4:160237400-160266200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr4:160237400-160274600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:160237600-160260000	Weak transcription	Fetal Thymus	thymus
39	chr4:160238200-160260000	Weak transcription	Fetal Brain Female	brain
40	chr4:160238600-160260200	Weak transcription	Pancreas	Pancrea
41	chr4:160238600-160263800	Weak transcription	Fetal Stomach	stomach
42	chr4:160238600-160263800	Weak transcription	Lung	lung
43	chr4:160238600-160282200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:160238800-160251000	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr4:160238800-160258200	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr4:160239600-160253400	Weak transcription	Brain Hippocampus Middle	brain
47	chr4:160240600-160260200	Weak transcription	Gastric	stomach
48	chr4:160241000-160281600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr4:160242400-160253400	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr4:160243000-160254600	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links