Variant report

Variant	rs562966
Chromosome Location	chr11:120076116-120076117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1287393	0.94[ASN][1000 genomes]
rs1287395	0.97[ASN][1000 genomes]
rs2444241	0.97[ASN][1000 genomes]
rs2444242	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2444243	0.98[ASN][1000 genomes]
rs2508495	0.98[ASN][1000 genomes]
rs2508496	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs476809	0.98[ASN][1000 genomes]
rs477863	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs489454	1.00[ASN][1000 genomes]
rs492275	1.00[ASN][1000 genomes]
rs513944	0.95[ASN][1000 genomes]
rs521841	1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs536743	0.95[ASN][1000 genomes]
rs537907	0.99[ASN][1000 genomes]
rs540857	0.99[ASN][1000 genomes]
rs547990	0.98[ASN][1000 genomes]
rs896695	0.98[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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv428581	chr11:120006048-120167603	Strong transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv518464	chr11:120040442-120109967	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs562966	PDZD3	cis	parietal	SCAN
rs562966	CCDC153	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120068800-120078400	Weak transcription	Small Intestine	intestine
2	chr11:120069800-120078400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:120070200-120077200	Weak transcription	Spleen	Spleen
4	chr11:120071400-120078400	Weak transcription	Brain Anterior Caudate	brain
5	chr11:120074400-120076800	Enhancers	NHDF-Ad	bronchial
6	chr11:120074400-120077200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:120074600-120079400	Weak transcription	Fetal Intestine Large	intestine
8	chr11:120074800-120078400	Weak transcription	Fetal Intestine Small	intestine
9	chr11:120074800-120078600	Weak transcription	Fetal Muscle Leg	muscle
10	chr11:120075200-120076200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr11:120075200-120076200	Enhancers	Esophagus	oesophagus
12	chr11:120075200-120076400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr11:120075200-120076800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:120075200-120076800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:120075200-120077000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:120075200-120077200	Enhancers	HMEC	breast
17	chr11:120075200-120081000	Enhancers	Pancreas	Pancrea
18	chr11:120075400-120077000	Weak transcription	Fetal Stomach	stomach
19	chr11:120075600-120076800	Enhancers	NHEK	skin
20	chr11:120075600-120078000	Weak transcription	Fetal Kidney	kidney
21	chr11:120075600-120078200	Weak transcription	Fetal Lung	lung
22	chr11:120075600-120078400	Enhancers	HepG2	liver
23	chr11:120075800-120076600	Enhancers	HSMMtube	muscle
24	chr11:120075800-120076800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:120075800-120076800	Enhancers	Muscle Satellite Cultured Cells	--
26	chr11:120075800-120076800	Enhancers	NHLF	lung
27	chr11:120075800-120078600	Enhancers	Liver	Liver
28	chr11:120076000-120076200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:120076000-120076200	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr11:120076000-120076200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr11:120076000-120076400	Enhancers	HSMM	muscle
32	chr11:120076000-120076400	Enhancers	NH-A	brain
33	chr11:120076000-120076600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr11:120076000-120076600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:120076000-120076600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr11:120076000-120076600	Enhancers	Osteobl	bone
37	chr11:120076000-120076800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr11:120076000-120078000	Enhancers	Monocytes-CD14+_RO01746	blood

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