Variant report

Variant	rs9600564
Chromosome Location	chr13:76435635-76435636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs7982226	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7982357	1.00[ASN][1000 genomes]
rs9530476	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9530480	0.85[ASN][1000 genomes]
rs9544027	1.00[JPT][hapmap]
rs9544062	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9544064	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9593136	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9600565	1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9600566	1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9600569	1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9600570	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9600576	1.00[JPT][hapmap];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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9600564	LMO7	cis	parietal	SCAN
rs9600564	SLAIN1	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76394400-76435800	Weak transcription	Colon Smooth Muscle	Colon
2	chr13:76396400-76436800	Weak transcription	Fetal Brain Male	brain
3	chr13:76406000-76436800	Strong transcription	Muscle Satellite Cultured Cells	--
4	chr13:76413200-76436800	Strong transcription	NHDF-Ad	bronchial
5	chr13:76413800-76437600	Strong transcription	HSMM	muscle
6	chr13:76417400-76443800	Weak transcription	Fetal Brain Female	brain
7	chr13:76417600-76436800	Weak transcription	Psoas Muscle	Psoas
8	chr13:76417600-76437800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:76417600-76444600	Weak transcription	HMEC	breast
10	chr13:76417800-76438800	Weak transcription	A549	lung
11	chr13:76424400-76444200	Weak transcription	Fetal Lung	lung
12	chr13:76427400-76440800	Weak transcription	Ovary	ovary
13	chr13:76428000-76444600	Weak transcription	Fetal Kidney	kidney
14	chr13:76428000-76444800	Weak transcription	Esophagus	oesophagus
15	chr13:76428200-76437400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr13:76428200-76444400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr13:76428400-76444600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr13:76428400-76444600	Weak transcription	Fetal Heart	heart
19	chr13:76429600-76444600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr13:76431000-76435800	Weak transcription	Fetal Stomach	stomach
21	chr13:76431000-76435800	Weak transcription	Fetal Thymus	thymus
22	chr13:76431000-76436800	Weak transcription	Gastric	stomach
23	chr13:76431000-76438400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr13:76431000-76444600	Weak transcription	Aorta	Aorta
25	chr13:76431200-76436600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:76431200-76436600	Weak transcription	Lung	lung
27	chr13:76431600-76436400	Weak transcription	Colonic Mucosa	Colon
28	chr13:76431600-76437600	Weak transcription	Duodenum Mucosa	Duodenum
29	chr13:76431600-76444600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr13:76431800-76436800	Weak transcription	Thymus	Thymus
31	chr13:76432000-76444600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr13:76432200-76436600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr13:76432200-76438000	Weak transcription	Left Ventricle	heart
34	chr13:76432200-76438800	Weak transcription	HepG2	liver
35	chr13:76432200-76443600	Weak transcription	Primary T cells from cord blood	blood
36	chr13:76432200-76444200	Weak transcription	GM12878-XiMat	blood
37	chr13:76432200-76444600	Weak transcription	Fetal Intestine Small	intestine
38	chr13:76432200-76444600	Weak transcription	Fetal Muscle Leg	muscle
39	chr13:76432200-76444600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr13:76432400-76437200	Weak transcription	Fetal Intestine Large	intestine
41	chr13:76433000-76444400	Weak transcription	Liver	Liver
42	chr13:76433400-76444200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr13:76434200-76437600	Weak transcription	Hela-S3	cervix
44	chr13:76434400-76436200	Enhancers	Placenta Amnion	Placenta Amnion
45	chr13:76434800-76436400	Weak transcription	NHLF	lung
46	chr13:76434800-76437800	Genic enhancers	Osteobl	bone
47	chr13:76435000-76436400	Genic enhancers	HSMMtube	muscle
48	chr13:76435000-76437400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr13:76435000-76439000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr13:76435000-76443800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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