Variant report

Variant	rs2058393
Chromosome Location	chr7:78857007-78857008
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10225262	1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes]
rs10230177	1.00[CEU][hapmap]
rs10234403	1.00[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs10235211	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10266537	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap]
rs10270040	1.00[CEU][hapmap]
rs10270764	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs10273845	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10480716	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10953797	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10953806	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10953812	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10953821	0.82[EUR][1000 genomes]
rs10953825	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs10953826	0.82[EUR][1000 genomes]
rs10953827	0.81[EUR][1000 genomes]
rs10953835	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs11532779	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11977493	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12111592	0.81[EUR][1000 genomes]
rs12111980	0.81[EUR][1000 genomes]
rs12154356	1.00[CEU][hapmap]
rs12154470	1.00[CEU][hapmap]
rs12216581	1.00[CEU][hapmap]
rs12532467	1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap]
rs12534590	1.00[CEU][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12539220	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs12540324	0.82[EUR][1000 genomes]
rs12666243	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs12706101	0.81[EUR][1000 genomes]
rs12706102	1.00[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs13222018	0.81[EUR][1000 genomes]
rs13224739	0.82[EUR][1000 genomes]
rs13230579	1.00[CEU][hapmap]
rs13237396	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13237397	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13240307	0.82[EUR][1000 genomes]
rs13243756	0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1358473	1.00[CEU][hapmap]
rs1406152	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs1406157	1.00[CEU][hapmap]
rs1406158	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1406159	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1528263	1.00[CEU][hapmap]
rs1528269	1.00[CEU][hapmap]
rs1528270	1.00[CEU][hapmap]
rs1528271	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1528272	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1528273	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1528274	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1528280	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1528281	0.82[EUR][1000 genomes]
rs1554833	1.00[CEU][hapmap]
rs1554834	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs1554835	1.00[CEU][hapmap]
rs1881292	1.00[CEU][hapmap]
rs1918936	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1918937	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1918938	0.82[EUR][1000 genomes]
rs1918939	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs2159709	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2242505	1.00[CEU][hapmap]
rs2364902	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs28757842	0.92[AMR][1000 genomes]
rs2886212	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs34066812	0.82[EUR][1000 genomes]
rs34263368	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4129689	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs4143262	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs4256536	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs4727838	1.00[CEU][hapmap]
rs4730746	1.00[CEU][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs4730747	1.00[CEU][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs60960798	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6466593	1.00[CEU][hapmap]
rs6946286	1.00[CEU][hapmap];0.81[JPT][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs6947782	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6950549	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6952164	1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes]
rs6953483	1.00[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6953771	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap]
rs6968269	0.92[AMR][1000 genomes]
rs71531164	0.82[EUR][1000 genomes]
rs717067	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7341488	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs7455235	0.93[AMR][1000 genomes]
rs7459140	1.00[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap]
rs7779953	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7781907	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7782460	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs7782585	1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap]
rs7805028	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9648980	1.00[CEU][hapmap]
rs9886146	0.81[EUR][1000 genomes]
rs9886330	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464598	chr7:78492642-79483480	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv607659	chr7:78492642-79483480	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1029799	chr7:78608097-79061737	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv888510	chr7:78742376-78865618	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv2757230	chr7:78801388-78887925	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv2759539	chr7:78801388-78887925	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	esv2761161	chr7:78805299-78857007	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
8	nsv437988	chr7:78806100-78910974	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1017352	chr7:78807175-78858690	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
10	nsv538989	chr7:78807175-78858690	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a
11	nsv831041	chr7:78819499-78973222	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2058393	MAGI2	cis	cerebellum	SCAN
rs2058393	TMEM120A	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:78855400-78858400	Weak transcription	Fetal Intestine Small	intestine
2	chr7:78855800-78857200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr7:78856000-78857200	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr7:78856200-78857400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr7:78856400-78857200	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr7:78856600-78857200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr7:78856600-78857800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr7:78856800-78858000	Weak transcription	HepG2	liver
9	chr7:78857000-78858000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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