Variant report

Variant	rs9576865
Chromosome Location	chr13:40140538-40140539
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1022808	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs1022810	0.82[CEU][hapmap]
rs1160321	0.94[TSI][hapmap]
rs1570414	0.93[CEU][hapmap]
rs1885758	1.00[CEU][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1885760	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1885762	0.85[EUR][1000 genomes]
rs1885763	0.82[CEU][hapmap]
rs2324347	0.85[TSI][hapmap]
rs2875329	1.00[CEU][hapmap]
rs3812881	0.81[CEU][hapmap]
rs3858867	0.89[TSI][hapmap]
rs4325425	1.00[CEU][hapmap]
rs4520717	1.00[CEU][hapmap]
rs4545673	0.90[MEX][hapmap]
rs4941933	0.85[EUR][1000 genomes]
rs4941935	0.85[EUR][1000 genomes]
rs4943674	0.86[EUR][1000 genomes]
rs61956469	0.82[EUR][1000 genomes]
rs6563719	0.82[CEU][hapmap]
rs6563720	1.00[CEU][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs6563726	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6563727	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7324883	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs7331023	1.00[CEU][hapmap];0.87[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7333587	0.93[CEU][hapmap]
rs7338428	0.87[EUR][1000 genomes]
rs7985507	0.98[EUR][1000 genomes]
rs7988729	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs912050	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs9285136	1.00[CEU][hapmap]
rs9315704	1.00[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs9315705	1.00[CEU][hapmap]
rs9532397	0.90[MEX][hapmap]
rs9548796	1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs9548807	0.85[EUR][1000 genomes]
rs9566448	0.87[CEU][hapmap];0.89[TSI][hapmap]
rs9566457	0.93[CEU][hapmap]
rs978135	1.00[CEU][hapmap];0.86[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9576865	ALG5	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40129000-40145600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:40129000-40152800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:40132200-40145600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr13:40135800-40142000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:40135800-40145600	Weak transcription	Lung	lung
6	chr13:40136400-40145600	Weak transcription	Right Ventricle	heart
7	chr13:40136800-40140800	Enhancers	Ovary	ovary
8	chr13:40136800-40141200	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr13:40137000-40140600	Enhancers	Fetal Heart	heart
10	chr13:40138800-40141600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr13:40138800-40152800	Weak transcription	Aorta	Aorta
12	chr13:40139000-40140600	Enhancers	Brain Anterior Caudate	brain
13	chr13:40139000-40140600	Enhancers	Fetal Lung	lung
14	chr13:40139200-40140600	Flanking Active TSS	NHEK	skin
15	chr13:40139200-40158000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr13:40139600-40140600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr13:40139600-40140600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr13:40139600-40141200	Enhancers	Rectal Smooth Muscle	rectum
19	chr13:40139800-40140600	Enhancers	NH-A	brain
20	chr13:40139800-40140800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr13:40139800-40140800	Enhancers	Left Ventricle	heart
22	chr13:40139800-40140800	Enhancers	Right Atrium	heart
23	chr13:40139800-40141200	Enhancers	NHLF	lung
24	chr13:40139800-40142000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr13:40139800-40142200	Enhancers	HSMMtube	muscle
26	chr13:40139800-40142200	Enhancers	NHDF-Ad	bronchial
27	chr13:40139800-40146400	Weak transcription	Brain Substantia Nigra	brain
28	chr13:40140000-40140600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr13:40140000-40140600	Enhancers	Brain Hippocampus Middle	brain
30	chr13:40140000-40145600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr13:40140000-40169400	Weak transcription	Fetal Stomach	stomach
32	chr13:40140200-40140600	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr13:40140200-40140600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr13:40140200-40140800	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr13:40140200-40140800	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr13:40140200-40140800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr13:40140200-40140800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr13:40140200-40140800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr13:40140200-40140800	Enhancers	Brain Cingulate Gyrus	brain
40	chr13:40140200-40141000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr13:40140200-40142200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr13:40140200-40145600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr13:40140200-40149600	Weak transcription	Fetal Muscle Leg	muscle
44	chr13:40140400-40140600	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr13:40140400-40140600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr13:40140400-40140600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr13:40140400-40140600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:40140400-40140600	Enhancers	A549	lung
49	chr13:40140400-40140800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr13:40140400-40140800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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