Variant report

Variant	rs10055018
Chromosome Location	chr5:80568957-80568958
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10071174	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10073527	0.82[EUR][1000 genomes]
rs10514216	0.89[EUR][1000 genomes]
rs11960275	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12516414	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12652649	0.86[ASN][1000 genomes]
rs13155580	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13172928	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16876403	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2270824	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2277037	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28819671	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4703828	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4703832	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4704709	0.82[EUR][1000 genomes]
rs4704717	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545	0.89[EUR][1000 genomes]
rs57086010	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59563495	0.84[ASN][1000 genomes]
rs60434474	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6872183	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10055018	CTD-2248H3.1	cis	lung	GTEx
rs10055018	CTC-281B15.1	cis	Thyroid	GTEx
rs10055018	CTC-281B15.1	cis	lung	GTEx
rs10055018	CTC-281B15.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80554600-80576400	Weak transcription	Pancreas	Pancrea
2	chr5:80560200-80570000	Weak transcription	Primary B cells from cord blood	blood
3	chr5:80565200-80580400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:80566000-80569800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:80566000-80572600	Weak transcription	Hela-S3	cervix
6	chr5:80566200-80570000	Weak transcription	Fetal Muscle Trunk	muscle
7	chr5:80566200-80574400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:80566200-80587800	Weak transcription	Ovary	ovary
9	chr5:80566400-80571200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:80566400-80572600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:80566400-80575400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:80566400-80581400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr5:80566400-80587600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:80566800-80570200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:80566800-80587600	Weak transcription	Right Ventricle	heart
16	chr5:80568000-80569400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:80568000-80585600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr5:80568800-80569000	ZNF genes & repeats	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links