Variant report

Variant	rs9600566
Chromosome Location	chr13:76445189-76445190
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AL359392.1-1	chr13:76445174-76445379	XLOC_010433

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs7982226	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7982357	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9530476	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9530480	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9544027	1.00[JPT][hapmap]
rs9544062	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9544064	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9593136	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9600564	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9600565	0.86[ASW][hapmap];0.95[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9600569	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9600570	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9600576	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[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	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv832649	chr13:76424872-76657891	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9600566	LMO7	cis	parietal	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76440000-76469200	Weak transcription	HSMM	muscle
2	chr13:76443200-76445400	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr13:76443400-76445600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr13:76444000-76445400	Active TSS	Osteobl	bone
5	chr13:76444200-76445200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr13:76444200-76445400	Active TSS	NHDF-Ad	bronchial
7	chr13:76444400-76445600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr13:76444400-76451000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr13:76444600-76445200	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr13:76444600-76445200	Active TSS	Muscle Satellite Cultured Cells	--
11	chr13:76444600-76445200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr13:76444600-76445200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr13:76444600-76445200	Active TSS	Brain Angular Gyrus	brain
14	chr13:76444600-76445200	Active TSS	Brain Anterior Caudate	brain
15	chr13:76444600-76445200	Active TSS	Brain Hippocampus Middle	brain
16	chr13:76444600-76445200	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr13:76444600-76445200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr13:76444600-76445200	Active TSS	Colon Smooth Muscle	Colon
19	chr13:76444600-76445200	Active TSS	Duodenum Mucosa	Duodenum
20	chr13:76444600-76445200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr13:76444600-76445200	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
22	chr13:76444600-76445200	Active TSS	Placenta	Placenta
23	chr13:76444600-76445200	Active TSS	Left Ventricle	heart
24	chr13:76444600-76445200	Active TSS	Ovary	ovary
25	chr13:76444600-76445200	Active TSS	Psoas Muscle	Psoas
26	chr13:76444600-76445200	Active TSS	Rectal Smooth Muscle	rectum
27	chr13:76444600-76445200	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr13:76444600-76445200	Enhancers	Thymus	Thymus
29	chr13:76444600-76445200	Flanking Active TSS	HUVEC	blood vessel
30	chr13:76444600-76445400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr13:76444600-76445400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr13:76444600-76445400	Active TSS	Aorta	Aorta
33	chr13:76444600-76445400	Active TSS	Fetal Lung	lung
34	chr13:76444600-76445400	Active TSS	Right Atrium	heart
35	chr13:76444600-76445400	Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr13:76444600-76445400	Active TSS	A549	lung
37	chr13:76444600-76445400	Active TSS	NHLF	lung
38	chr13:76444600-76445600	Active TSS	Adipose Nuclei	Adipose
39	chr13:76444600-76445600	Active TSS	Brain Substantia Nigra	brain
40	chr13:76444600-76445600	Active TSS	Fetal Muscle Trunk	muscle
41	chr13:76444600-76449600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr13:76444800-76445200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr13:76444800-76445200	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
44	chr13:76444800-76445200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr13:76444800-76445200	Enhancers	Stomach Mucosa	stomach
46	chr13:76444800-76445400	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr13:76444800-76445400	Weak transcription	Fetal Brain Female	brain
48	chr13:76444800-76445400	Active TSS	HepG2	liver
49	chr13:76444800-76449000	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr13:76444800-76450400	Weak transcription	Fetal Heart	heart

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