Variant report

Variant	rs6506539
Chromosome Location	chr18:7904331-7904332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12606453	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12960805	0.80[JPT][hapmap]
rs1440997	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1866854	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2165910	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9676009	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs9961274	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534374	chr18:7438812-8412546	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv458016	chr18:7488133-7934001	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv576399	chr18:7488133-7934001	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2762810	chr18:7492090-7924728	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1062911	chr18:7561991-8088274	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv543637	chr18:7561991-8088274	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1064345	chr18:7562051-8088274	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv543638	chr18:7562051-8088274	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:7857800-7907200	Weak transcription	Thymus	Thymus
2	chr18:7886800-7914200	Weak transcription	HepG2	liver
3	chr18:7890000-7905600	Weak transcription	Fetal Thymus	thymus
4	chr18:7890000-7907200	Weak transcription	Lung	lung
5	chr18:7897000-7905400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr18:7897400-7913200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr18:7898000-7915200	Weak transcription	Fetal Heart	heart
8	chr18:7898600-7907600	Weak transcription	Aorta	Aorta
9	chr18:7898800-7904400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr18:7899000-7908600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr18:7899000-7916200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr18:7901400-7906200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr18:7901600-7904600	Enhancers	NHLF	lung
14	chr18:7901600-7905200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr18:7902600-7909000	Weak transcription	Pancreas	Pancrea
16	chr18:7902800-7904600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr18:7903400-7905000	Enhancers	Muscle Satellite Cultured Cells	--
18	chr18:7903400-7905600	Weak transcription	Left Ventricle	heart
19	chr18:7903400-7905600	Weak transcription	Right Ventricle	heart
20	chr18:7903400-7908000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr18:7903400-7909000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr18:7903400-7910200	Weak transcription	Ovary	ovary
23	chr18:7903400-7914800	Weak transcription	Adipose Nuclei	Adipose
24	chr18:7903400-7915200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr18:7903400-7922200	Weak transcription	Right Atrium	heart
26	chr18:7903400-7922200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr18:7903600-7905000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr18:7903600-7907200	Weak transcription	Psoas Muscle	Psoas
29	chr18:7904000-7904400	Weak transcription	Colon Smooth Muscle	Colon
30	chr18:7904200-7904600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr18:7904200-7904600	Flanking Active TSS	A549	lung
32	chr18:7904200-7904800	Enhancers	NH-A	brain
33	chr18:7904200-7904800	Enhancers	NHDF-Ad	bronchial
34	chr18:7904200-7904800	Enhancers	Osteobl	bone
35	chr18:7904200-7905200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr18:7904200-7905400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr18:7904200-7905600	Enhancers	Hela-S3	cervix
38	chr18:7904200-7905800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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