Variant report

Variant	rs28819671
Chromosome Location	chr5:80565952-80565953
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10036376	0.84[EUR][1000 genomes]
rs10055018	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10071174	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10073527	0.87[EUR][1000 genomes]
rs10074794	0.83[EUR][1000 genomes]
rs10514215	0.84[EUR][1000 genomes]
rs10514216	0.94[EUR][1000 genomes]
rs11960275	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12516414	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12652649	0.86[ASN][1000 genomes]
rs13155580	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs13170098	0.84[EUR][1000 genomes]
rs13172928	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16876403	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2270824	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2277037	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4703828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4703832	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4704709	0.87[EUR][1000 genomes]
rs4704717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545	0.94[EUR][1000 genomes]
rs57086010	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59563495	0.84[ASN][1000 genomes]
rs60434474	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6872183	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7448717	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28819671	CTD-2248H3.1	cis	lung	GTEx
rs28819671	CTC-281B15.1	cis	Thyroid	GTEx
rs28819671	CTC-281B15.1	cis	lung	GTEx
rs28819671	CTC-281B15.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80548800-80568000	Strong transcription	Skeletal Muscle Female	skeletal muscle
2	chr5:80552800-80567200	Weak transcription	Brain Anterior Caudate	brain
3	chr5:80554600-80576400	Weak transcription	Pancreas	Pancrea
4	chr5:80555200-80568600	Weak transcription	Fetal Stomach	stomach
5	chr5:80558200-80568000	Strong transcription	Skeletal Muscle Male	skeletal muscle
6	chr5:80559600-80568400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:80559800-80567200	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:80560000-80566000	Weak transcription	Ovary	ovary
9	chr5:80560200-80570000	Weak transcription	Primary B cells from cord blood	blood
10	chr5:80560400-80567200	Weak transcription	Primary T cells from cord blood	blood
11	chr5:80563600-80567400	Weak transcription	Brain Substantia Nigra	brain
12	chr5:80563600-80567400	Weak transcription	Psoas Muscle	Psoas
13	chr5:80563800-80566400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:80564000-80566200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:80564200-80566000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:80564200-80566000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr5:80564200-80566000	Enhancers	NHDF-Ad	bronchial
18	chr5:80564200-80566000	Enhancers	NHLF	lung
19	chr5:80564200-80566000	Enhancers	Osteobl	bone
20	chr5:80564200-80566200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr5:80564200-80566400	Enhancers	HepG2	liver
22	chr5:80564400-80566000	Enhancers	Hela-S3	cervix
23	chr5:80564400-80566200	Enhancers	A549	lung
24	chr5:80564400-80566400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:80564400-80566600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr5:80564600-80566200	Strong transcription	Left Ventricle	heart
27	chr5:80564800-80566000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:80564800-80566200	Enhancers	Gastric	stomach
29	chr5:80564800-80566800	ZNF genes & repeats	Aorta	Aorta
30	chr5:80565000-80566200	Enhancers	GM12878-XiMat	blood
31	chr5:80565000-80566400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr5:80565000-80566400	Weak transcription	Fetal Heart	heart
33	chr5:80565000-80568400	Weak transcription	Brain Hippocampus Middle	brain
34	chr5:80565200-80566000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:80565200-80566200	Enhancers	Primary B cells from peripheral blood	blood
36	chr5:80565200-80580400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:80565400-80566800	Strong transcription	Right Ventricle	heart
38	chr5:80565600-80566200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr5:80565600-80566200	Enhancers	H9 Cell Line	embryonic stem cell
40	chr5:80565600-80566200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:80565600-80566200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr5:80565600-80566200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr5:80565600-80566200	Strong transcription	Fetal Muscle Trunk	muscle
44	chr5:80565600-80566400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr5:80565600-80566600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr5:80565600-80566800	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr5:80565600-80566800	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr5:80565800-80566000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr5:80565800-80566000	Enhancers	Adipose Nuclei	Adipose
50	chr5:80565800-80566000	Enhancers	Lung	lung

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