Variant report

Variant	rs6563720
Chromosome Location	chr13:40098890-40098891
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1022808	1.00[CEU][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1022810	0.82[CEU][hapmap]
rs1160321	1.00[GIH][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs1570414	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs1885758	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1885760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1885762	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1885763	0.82[CEU][hapmap]
rs2324333	0.88[CHB][hapmap];1.00[ASN][1000 genomes]
rs2324335	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2324347	1.00[GIH][hapmap];0.84[MEX][hapmap]
rs2875329	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3812881	0.81[CEU][hapmap]
rs3858867	1.00[GIH][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap]
rs4304917	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4325425	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4471557	1.00[ASN][1000 genomes]
rs4520717	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4559795	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4941933	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941935	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4943674	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6563719	0.82[CEU][hapmap]
rs6563721	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6563726	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6563727	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7319551	0.86[GIH][hapmap]
rs7324883	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7331023	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7333587	0.93[CEU][hapmap];0.84[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7335390	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7981205	0.80[EUR][1000 genomes]
rs7985507	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7986918	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7988729	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs8000471	0.88[CHB][hapmap];1.00[ASN][1000 genomes]
rs912050	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs927515	1.00[GIH][hapmap];0.84[MEX][hapmap]
rs9285135	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9285136	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9315698	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9315704	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9315705	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs9548796	1.00[CEU][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9548807	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9566448	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9566457	0.93[CEU][hapmap];0.81[AMR][1000 genomes]
rs9576865	1.00[CEU][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs978135	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754118	chr13:39347702-40222644	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers 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	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
3	esv2761784	chr13:40086325-40100095	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases
4	nsv1050137	chr13:40090742-40118499	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6563720	ALG5	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40077600-40101400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:40090600-40100800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr13:40090600-40102400	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr13:40090800-40102400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:40093800-40100800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr13:40096200-40099000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr13:40096200-40099600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr13:40096200-40101600	Weak transcription	Brain Angular Gyrus	brain
9	chr13:40096600-40101400	Weak transcription	Aorta	Aorta
10	chr13:40096800-40099200	Weak transcription	Right Ventricle	heart
11	chr13:40096800-40100600	Weak transcription	Ovary	ovary
12	chr13:40096800-40101400	Weak transcription	Right Atrium	heart
13	chr13:40096800-40102000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr13:40096800-40110400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:40097000-40101200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr13:40097200-40099600	Weak transcription	Fetal Heart	heart
17	chr13:40097600-40099400	Weak transcription	Left Ventricle	heart
18	chr13:40097800-40099800	Enhancers	Fetal Lung	lung
19	chr13:40098200-40099000	Enhancers	NHEK	skin
20	chr13:40098600-40099400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr13:40098600-40099400	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr13:40098600-40101200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr13:40098800-40099400	Enhancers	Brain Substantia Nigra	brain
24	chr13:40098800-40101200	Weak transcription	HMEC	breast
25	chr13:40098800-40102000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr13:40098800-40102400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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