Variant report

Variant	rs4832289
Chromosome Location	chr2:86673094-86673095
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10185085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1036940	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs11127040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11127042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1116326	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11690696	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11693352	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11903855	1.00[CHB][hapmap]
rs12475983	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12476666	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12714187	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12995117	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1468039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1518811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2030259	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2044230	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2139150	1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs218060	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs2367575	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs308901	0.87[CHD][hapmap]
rs308907	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs308913	1.00[JPT][hapmap];1.00[LWK][hapmap]
rs396354	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs433655	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4832284	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832287	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4832288	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4832290	0.95[CEU][hapmap];0.87[CHD][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4832293	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4832294	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6547688	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547689	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547690	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6547700	0.87[CHD][hapmap]
rs6710124	1.00[CHB][hapmap]
rs6714826	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs6742018	1.00[JPT][hapmap];1.00[YRI][hapmap]
rs683139	0.87[CHD][hapmap]
rs7574389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598058	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs950780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs966477	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[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	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4832289	KDM3A	cis	parietal	SCAN
rs4832289	RNF103	cis	cerebellum	SCAN
rs4832289	ST3GAL5	cis	parietal	SCAN
rs4832289	IMMT	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86669800-86678600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:86669800-86679200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:86670000-86678200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr2:86670000-86684200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:86670400-86676400	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr2:86670400-86693400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr2:86670600-86674000	Strong transcription	Placenta	Placenta
8	chr2:86670600-86674200	Genic enhancers	Primary T cells fromperipheralblood	blood
9	chr2:86670600-86675200	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:86670600-86676400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
11	chr2:86670800-86674200	Strong transcription	Muscle Satellite Cultured Cells	--
12	chr2:86670800-86675800	Weak transcription	HUVEC	blood vessel
13	chr2:86670800-86676200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:86670800-86676400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:86670800-86676600	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr2:86670800-86677200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr2:86670800-86678600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:86670800-86681000	Weak transcription	Stomach Mucosa	stomach
19	chr2:86670800-86684200	Weak transcription	Colonic Mucosa	Colon
20	chr2:86671000-86673200	Enhancers	Hela-S3	cervix
21	chr2:86671000-86673400	Enhancers	Brain Hippocampus Middle	brain
22	chr2:86671000-86673600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr2:86671000-86673800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr2:86671000-86676800	Weak transcription	NH-A	brain
25	chr2:86671000-86676800	Weak transcription	Osteobl	bone
26	chr2:86671000-86677200	Weak transcription	Fetal Kidney	kidney
27	chr2:86671000-86725600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:86671200-86676400	Weak transcription	NHEK	skin
29	chr2:86671200-86677000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:86671200-86689400	Strong transcription	Primary B cells from cord blood	blood
31	chr2:86671400-86673200	Enhancers	Colon Smooth Muscle	Colon
32	chr2:86671400-86673600	Weak transcription	Fetal Stomach	stomach
33	chr2:86671400-86676800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr2:86671400-86676800	Weak transcription	NHDF-Ad	bronchial
35	chr2:86671400-86677200	Genic enhancers	HepG2	liver
36	chr2:86671400-86677400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
37	chr2:86671400-86678000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
38	chr2:86671400-86678200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:86671400-86684200	Weak transcription	Gastric	stomach
40	chr2:86671400-86685600	Weak transcription	Esophagus	oesophagus
41	chr2:86671400-86687800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr2:86671400-86722600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:86671400-86725600	Strong transcription	A549	lung
44	chr2:86671600-86673200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr2:86671600-86673200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr2:86671600-86673200	Enhancers	Brain Anterior Caudate	brain
47	chr2:86671600-86673200	Enhancers	Stomach Smooth Muscle	stomach
48	chr2:86671600-86673400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr2:86671600-86673600	Weak transcription	Aorta	Aorta
50	chr2:86671600-86673600	Strong transcription	K562	blood

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