Variant report

Variant	rs11575494
Chromosome Location	chr7:50538052-50538053
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:50537654..50539269-chr7:50553300..50555389,2	K562	blood:

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10499693	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575293	1.00[EUR][1000 genomes]
rs11575302	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575340	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575343	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575360	1.00[EUR][1000 genomes]
rs11575381	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575385	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575407	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575447	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575493	1.00[EUR][1000 genomes]
rs11575501	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575502	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575503	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575504	1.00[EUR][1000 genomes]
rs11575505	1.00[CEU][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575507	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575508	1.00[EUR][1000 genomes]
rs11575510	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575511	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575512	1.00[EUR][1000 genomes]
rs11575514	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575518	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575519	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11575522	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575523	1.00[EUR][1000 genomes]
rs11575527	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575535	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs11575537	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11575540	1.00[EUR][1000 genomes]
rs11575542	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575543	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11575546	1.00[EUR][1000 genomes]
rs11575547	1.00[EUR][1000 genomes]
rs11575549	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11978797	0.92[EUR][1000 genomes]
rs11981575	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11982708	1.00[EUR][1000 genomes]
rs11982772	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11982776	0.92[EUR][1000 genomes]
rs11983581	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs11983757	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs12112308	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12113897	0.84[EUR][1000 genomes]
rs2329370	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3173669	0.92[EUR][1000 genomes]
rs55869201	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55992615	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56030652	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56951986	0.85[AMR][1000 genomes]
rs57167849	0.92[EUR][1000 genomes]
rs57835901	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57927451	0.85[AMR][1000 genomes]
rs59150746	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59828622	0.92[EUR][1000 genomes]
rs6956737	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6975312	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6978556	0.92[EUR][1000 genomes]
rs73695512	1.00[EUR][1000 genomes]
rs73695638	0.84[EUR][1000 genomes]
rs73695639	0.92[EUR][1000 genomes]
rs73695640	0.92[EUR][1000 genomes]
rs73695641	0.92[EUR][1000 genomes]
rs73695643	0.92[EUR][1000 genomes]
rs73695661	0.92[EUR][1000 genomes]
rs73695664	0.92[EUR][1000 genomes]
rs73695666	0.92[EUR][1000 genomes]
rs73695667	0.92[EUR][1000 genomes]
rs73695668	0.92[EUR][1000 genomes]
rs73695669	0.92[EUR][1000 genomes]
rs73695670	0.92[EUR][1000 genomes]
rs73695671	0.92[EUR][1000 genomes]
rs73695672	0.92[EUR][1000 genomes]
rs73695673	0.92[EUR][1000 genomes]
rs73695681	1.00[EUR][1000 genomes]
rs73695682	1.00[EUR][1000 genomes]
rs73695683	1.00[EUR][1000 genomes]
rs73695684	1.00[EUR][1000 genomes]
rs73695700	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695701	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73695702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73697528	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73697574	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs930707	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9942578	0.92[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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1026081	chr7:50525900-50538184	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11575494	PGAM2	trans	brain	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50535800-50539000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr7:50535800-50540800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr7:50535800-50546800	Weak transcription	Pancreas	Pancrea
4	chr7:50535800-50553200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:50536000-50542800	Weak transcription	Colonic Mucosa	Colon
6	chr7:50536200-50541400	Weak transcription	HepG2	liver
7	chr7:50536200-50542200	Strong transcription	Fetal Intestine Small	intestine
8	chr7:50536200-50545400	Weak transcription	Right Atrium	heart
9	chr7:50536400-50541400	Weak transcription	Colon Smooth Muscle	Colon
10	chr7:50536400-50541600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr7:50536400-50541800	Strong transcription	Fetal Intestine Large	intestine
12	chr7:50536600-50543000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr7:50537200-50538200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr7:50537800-50538600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr7:50538000-50538200	Enhancers	H1 Cell Line	embryonic stem cell
16	chr7:50538000-50538200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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