Variant report

Variant	rs9566448
Chromosome Location	chr13:40090409-40090410
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1022808	0.87[CEU][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1160321	0.86[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes]
rs1570414	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs1570417	0.82[AFR][1000 genomes]
rs1885758	0.87[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs1885760	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1885762	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2324333	0.88[CHB][hapmap];0.97[ASN][1000 genomes]
rs2324335	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2324347	0.86[GIH][hapmap];0.94[MEX][hapmap]
rs2875329	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs3858867	0.86[GIH][hapmap];0.94[MEX][hapmap]
rs4304917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4325425	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4471557	0.97[ASN][1000 genomes]
rs4520717	0.87[CEU][hapmap];0.90[AMR][1000 genomes]
rs4559795	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4941933	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4941935	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4943674	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61956469	0.81[AMR][1000 genomes]
rs6563720	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]
rs6563721	0.83[AMR][1000 genomes]
rs6563726	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6563727	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs7319551	1.00[GIH][hapmap]
rs7324883	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs7331023	0.87[CEU][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs7333587	0.81[CEU][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs7335390	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7985507	0.83[AMR][1000 genomes]
rs7986918	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7988729	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs8000471	0.88[CHB][hapmap];0.97[ASN][1000 genomes]
rs912050	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs927515	0.86[GIH][hapmap];0.94[MEX][hapmap]
rs9285135	0.83[AMR][1000 genomes]
rs9285136	0.87[CEU][hapmap];0.83[AMR][1000 genomes]
rs9315698	0.84[AMR][1000 genomes]
rs9315704	0.87[CEU][hapmap];0.89[CHB][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs9315705	0.87[CEU][hapmap]
rs9548796	0.87[CEU][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9548807	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9566457	0.81[CEU][hapmap]
rs9576865	0.87[CEU][hapmap];0.89[TSI][hapmap]
rs978135	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv2757529	chr13:40040036-40090742	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
4	esv2759933	chr13:40040036-40090742	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1049669	chr13:40081362-40095803	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases
6	esv2761784	chr13:40086325-40100095	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9566448	ALG5	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40074200-40094400	Weak transcription	Adipose Nuclei	Adipose
2	chr13:40076400-40096000	Weak transcription	Lung	lung
3	chr13:40077600-40101400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr13:40081600-40096000	Weak transcription	Fetal Lung	lung
5	chr13:40081600-40096600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:40088000-40090800	Enhancers	Left Ventricle	heart
7	chr13:40088000-40090800	Enhancers	Right Ventricle	heart
8	chr13:40088200-40090600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr13:40088200-40091600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr13:40088400-40090600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:40088400-40090600	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr13:40088400-40090600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:40088400-40091000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr13:40088400-40091000	Enhancers	Fetal Muscle Leg	muscle
15	chr13:40088400-40091000	Enhancers	Right Atrium	heart
16	chr13:40088400-40091600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr13:40088600-40090800	Enhancers	H1 Cell Line	embryonic stem cell
18	chr13:40088600-40090800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr13:40088600-40090800	Enhancers	Aorta	Aorta
20	chr13:40088600-40090800	Enhancers	HSMMtube	muscle
21	chr13:40088600-40091000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr13:40088800-40090800	Enhancers	Fetal Brain Female	brain
23	chr13:40089200-40090600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr13:40089200-40090800	Enhancers	Brain Substantia Nigra	brain
25	chr13:40089400-40090600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:40089400-40090600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr13:40089400-40090600	Enhancers	NH-A	brain
28	chr13:40089400-40091200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr13:40089600-40091000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr13:40089600-40091000	Enhancers	Colon Smooth Muscle	Colon
31	chr13:40089600-40091000	Enhancers	Fetal Brain Male	brain
32	chr13:40089600-40091200	Enhancers	Brain Hippocampus Middle	brain
33	chr13:40089800-40090600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr13:40089800-40090800	Enhancers	Osteobl	bone
35	chr13:40089800-40091200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr13:40090000-40091000	Enhancers	HMEC	breast
37	chr13:40090000-40091200	Flanking Active TSS	Fetal Heart	heart
38	chr13:40090000-40091200	Enhancers	NHDF-Ad	bronchial
39	chr13:40090200-40090600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr13:40090200-40090600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr13:40090200-40090800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr13:40090200-40090800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:40090200-40090800	Enhancers	Ovary	ovary
44	chr13:40090200-40090800	Enhancers	NHEK	skin
45	chr13:40090200-40091000	Enhancers	Brain Anterior Caudate	brain
46	chr13:40090200-40091000	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr13:40090200-40091000	Enhancers	HSMM	muscle
48	chr13:40090200-40091200	Enhancers	Brain Cingulate Gyrus	brain
49	chr13:40090400-40090600	Enhancers	Stomach Smooth Muscle	stomach
50	chr13:40090400-40090800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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