Variant report

Variant	rs6473840
Chromosome Location	chr8:54434247-54434248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10095702	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10958370	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1477956	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1477957	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17361507	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1904072	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6473839	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6473842	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7004273	0.89[ASN][1000 genomes]
rs7812717	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7829521	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752674	chr8:54181147-54483747	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6473840	RP11-1081M5.1	cis	Artery Aorta	GTEx
rs6473840	RP11-1081M5.2	cis	Artery Tibial	GTEx
rs6473840	RP11-1081M5.1	cis	Artery Tibial	GTEx

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54419200-54436200	Weak transcription	Pancreas	Pancrea
2	chr8:54421800-54434800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:54422800-54434800	Weak transcription	Esophagus	oesophagus
4	chr8:54426400-54434600	Weak transcription	Fetal Muscle Leg	muscle
5	chr8:54427400-54434600	Weak transcription	NHLF	lung
6	chr8:54427800-54436200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr8:54428000-54434400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr8:54428200-54435000	Weak transcription	Fetal Stomach	stomach
9	chr8:54428800-54435200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr8:54429200-54434600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr8:54430600-54436000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:54432800-54434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr8:54433200-54434600	Enhancers	NHEK	skin
14	chr8:54433400-54434400	Enhancers	A549	lung
15	chr8:54433400-54434600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr8:54433400-54435200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr8:54433400-54436400	Flanking Active TSS	Osteobl	bone
18	chr8:54433400-54437000	Active TSS	Right Ventricle	heart
19	chr8:54433400-54437200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr8:54433600-54435400	Flanking Active TSS	NH-A	brain
21	chr8:54433600-54435600	Active TSS	Stomach Smooth Muscle	stomach
22	chr8:54433600-54436000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr8:54433600-54436000	Active TSS	Left Ventricle	heart
24	chr8:54433600-54437000	Active TSS	Aorta	Aorta
25	chr8:54433800-54434800	Enhancers	NHDF-Ad	bronchial
26	chr8:54433800-54435000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr8:54433800-54435200	Active TSS	Fetal Heart	heart
28	chr8:54433800-54435200	Enhancers	Stomach Mucosa	stomach
29	chr8:54433800-54436200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr8:54433800-54436600	Active TSS	Fetal Thymus	thymus
31	chr8:54433800-54437200	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr8:54433800-54437400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr8:54434000-54434400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr8:54434000-54434400	Enhancers	Rectal Smooth Muscle	rectum
35	chr8:54434000-54434400	Enhancers	HSMMtube	muscle
36	chr8:54434000-54434600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr8:54434000-54434600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr8:54434000-54434800	Weak transcription	Gastric	stomach
39	chr8:54434000-54435800	Active TSS	HSMM	muscle
40	chr8:54434000-54437000	Active TSS	Ovary	ovary
41	chr8:54434200-54434400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr8:54434200-54434600	Weak transcription	HUVEC	blood vessel
43	chr8:54434200-54435000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr8:54434200-54436000	Active TSS	Colon Smooth Muscle	Colon
45	chr8:54434200-54437000	Flanking Active TSS	HMEC	breast
46	chr8:54434200-54437600	Active TSS	Duodenum Smooth Muscle	Duodenum

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