Variant report

Variant	rs2746349
Chromosome Location	chr1:57126650-57126651
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10749708	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10789036	1.00[ASW][hapmap];0.84[LWK][hapmap];0.81[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap]
rs10789038	0.88[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10789040	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10789041	0.84[AMR][1000 genomes]
rs10889006	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10889008	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[LWK][hapmap];0.81[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10889009	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11206872	0.83[ASN][1000 genomes]
rs11206885	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11206888	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11206889	1.00[ASW][hapmap];0.81[CEU][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11206890	1.00[ASW][hapmap];0.85[CEU][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11206895	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1124900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11804779	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12023668	0.81[AMR][1000 genomes]
rs12048572	0.81[AMR][1000 genomes]
rs12070903	0.81[AMR][1000 genomes]
rs12072057	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12073311	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12078260	1.00[ASW][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];0.81[TSI][hapmap]
rs12092267	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12097148	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12738355	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13374924	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs1418442	0.81[CEU][hapmap]
rs2064421	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2064422	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2092594	0.85[EUR][1000 genomes]
rs2092595	0.92[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[EUR][1000 genomes]
rs2143754	0.96[CEU][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs2245475	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2404718	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2404986	0.83[ASN][1000 genomes]
rs2404987	0.94[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs2404994	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2746338	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2746339	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2746345	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2746348	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[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2746351	0.85[EUR][1000 genomes]
rs2746353	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2796491	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2796492	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2796493	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2796495	1.00[CEU][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2796496	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2796498	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2796499	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2796506	0.85[EUR][1000 genomes]
rs2796507	0.85[EUR][1000 genomes]
rs2796509	0.96[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[EUR][1000 genomes]
rs2796511	0.85[EUR][1000 genomes]
rs2796512	0.96[CEU][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs2796514	0.85[EUR][1000 genomes]
rs2796517	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2796519	0.85[CEU][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2796523	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2796527	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2796534	0.96[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2796541	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4551620	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4584419	1.00[ASW][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap]
rs59223968	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61772962	0.83[AMR][1000 genomes]
rs61774288	0.83[ASN][1000 genomes]
rs6588641	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6588643	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671760	0.82[AMR][1000 genomes]
rs6683935	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs715404	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs715405	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7415042	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap]
rs7419053	0.81[CEU][hapmap];0.82[MEX][hapmap]
rs7515414	0.81[CEU][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs7519509	1.00[ASW][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.89[TSI][hapmap]
rs7547486	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs857132	0.82[EUR][1000 genomes]
rs857147	0.92[CEU][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs857148	0.92[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs857150	0.83[EUR][1000 genomes]
rs857155	0.96[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs857156	0.84[EUR][1000 genomes]
rs857159	0.82[EUR][1000 genomes]
rs932447	0.81[CEU][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs963528	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9887834	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9887940	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][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	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv523032	chr1:57116909-57249558	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2746349	TMEM48	cis	parietal	SCAN
rs2746349	C1orf175	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57120000-57132800	Weak transcription	Right Atrium	heart
2	chr1:57122400-57129200	Weak transcription	Psoas Muscle	Psoas
3	chr1:57122800-57128600	Weak transcription	HepG2	liver
4	chr1:57122800-57169600	Weak transcription	Ovary	ovary
5	chr1:57123000-57131400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:57123000-57141800	Weak transcription	Hela-S3	cervix
7	chr1:57123000-57142000	Weak transcription	A549	lung
8	chr1:57123000-57143400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:57125400-57127200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr1:57125600-57169800	Weak transcription	Aorta	Aorta
11	chr1:57126200-57127000	Enhancers	Skeletal Muscle Male	skeletal muscle
12	chr1:57126400-57130400	Weak transcription	Fetal Heart	heart
13	chr1:57126600-57126800	Enhancers	Gastric	stomach
14	chr1:57126600-57126800	Enhancers	Left Ventricle	heart
15	chr1:57126600-57127000	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links