Variant report

Variant	rs60488995
Chromosome Location	chr5:80566680-80566681
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10038684	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041063	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053706	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055063	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10056565	0.83[ASN][1000 genomes]
rs10063615	0.83[ASN][1000 genomes]
rs10066296	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078279	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474656	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514213	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1055383	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10942945	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950033	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13362314	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566432	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17294418	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2270823	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406556	0.83[ASN][1000 genomes]
rs28464111	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650401	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897389	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2897390	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703827	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704707	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704708	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704710	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704712	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704715	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704720	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59132806	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60904680	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61244991	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365865	0.83[ASN][1000 genomes]
rs68077638	0.83[ASN][1000 genomes]
rs6866499	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6867884	0.83[ASN][1000 genomes]
rs6885028	0.83[ASN][1000 genomes]
rs6893467	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130869	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7381116	0.87[AMR][1000 genomes]
rs7709071	0.83[ASN][1000 genomes]
rs7709149	0.83[ASN][1000 genomes]
rs7720009	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728465	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7734902	0.83[ASN][1000 genomes]
rs9293841	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs60488995	CTD-2248H3.1	cis	Esophagus Mucosa	GTEx
rs60488995	CTD-2248H3.1	cis	Esophagus Muscularis	GTEx
rs60488995	CTD-2248H3.1	cis	lung	GTEx
rs60488995	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs60488995	CTC-281B15.1	cis	Thyroid	GTEx
rs60488995	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs60488995	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs60488995	CTD-2248H3.1	cis	Thyroid	GTEx
rs60488995	CTC-281B15.1	cis	Stomach	GTEx
rs60488995	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs60488995	CTC-281B15.1	cis	lung	GTEx
rs60488995	CTC-281B15.1	cis	Artery Aorta	GTEx
rs60488995	CTD-2248H3.1	cis	Artery Aorta	GTEx

Chromatin state (count:39 , 50 per page) page: 1

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	chr5:80560200-80570000	Weak transcription	Primary B cells from cord blood	blood
9	chr5:80560400-80567200	Weak transcription	Primary T cells from cord blood	blood
10	chr5:80563600-80567400	Weak transcription	Brain Substantia Nigra	brain
11	chr5:80563600-80567400	Weak transcription	Psoas Muscle	Psoas
12	chr5:80564800-80566800	ZNF genes & repeats	Aorta	Aorta
13	chr5:80565000-80568400	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:80565200-80580400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:80565400-80566800	Strong transcription	Right Ventricle	heart
16	chr5:80565600-80566800	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr5:80565600-80566800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr5:80565800-80566800	Enhancers	H1 Cell Line	embryonic stem cell
19	chr5:80565800-80566800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr5:80565800-80566800	Enhancers	Fetal Thymus	thymus
21	chr5:80566000-80566800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:80566000-80569800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr5:80566000-80572600	Weak transcription	Hela-S3	cervix
24	chr5:80566200-80566800	ZNF genes & repeats	Left Ventricle	heart
25	chr5:80566200-80567200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:80566200-80567600	Enhancers	Dnd41	blood
27	chr5:80566200-80570000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr5:80566200-80574400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:80566200-80587800	Weak transcription	Ovary	ovary
30	chr5:80566400-80566800	Enhancers	HUES6 Cell Line	embryonic stem cell
31	chr5:80566400-80566800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr5:80566400-80567800	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr5:80566400-80571200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr5:80566400-80572600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:80566400-80575400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:80566400-80581400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:80566400-80587600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:80566600-80567200	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr5:80566600-80567200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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