Variant report

Variant	rs28464111
Chromosome Location	chr5:80613197-80613198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10038684	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10041063	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053706	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055063	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10056565	0.83[ASN][1000 genomes]
rs10063615	0.83[ASN][1000 genomes]
rs10066296	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078279	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474656	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514213	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1055383	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10942945	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950033	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13362314	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566432	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17294418	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2270823	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2406556	0.83[ASN][1000 genomes]
rs28650401	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897389	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2897390	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703827	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704707	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704708	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704710	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704712	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704715	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704720	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59132806	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60488995	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60904680	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61244991	0.87[AFR][1000 genomes];0.97[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	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6867884	0.83[ASN][1000 genomes]
rs6885028	0.83[ASN][1000 genomes]
rs6893467	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130869	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7381116	0.89[AMR][1000 genomes]
rs7709071	0.83[ASN][1000 genomes]
rs7709149	0.83[ASN][1000 genomes]
rs7720009	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728465	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7734902	0.83[ASN][1000 genomes]
rs9293841	0.92[AMR][1000 genomes];0.86[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	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs28464111	CTC-281B15.1	cis	lung	GTEx
rs28464111	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs28464111	CTD-2248H3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs28464111	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs28464111	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs28464111	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs28464111	CTC-281B15.1	cis	Thyroid	GTEx
rs28464111	CTC-281B15.1	cis	Stomach	GTEx
rs28464111	CTD-2248H3.1	cis	Esophagus Muscularis	GTEx
rs28464111	CTD-2248H3.1	cis	Artery Aorta	GTEx
rs28464111	CTD-2248H3.1	cis	lung	GTEx
rs28464111	CTD-2248H3.1	cis	Thyroid	GTEx
rs28464111	CTC-281B15.1	cis	Artery Aorta	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80608600-80615800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr5:80608600-80623000	Weak transcription	Psoas Muscle	Psoas
3	chr5:80609800-80613400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr5:80609800-80613600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:80610000-80614600	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr5:80610000-80618000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:80610600-80621800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:80610800-80613400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:80611200-80616000	Weak transcription	Liver	Liver
10	chr5:80611400-80613200	Weak transcription	Left Ventricle	heart
11	chr5:80611400-80614400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:80611600-80613200	Weak transcription	Primary T cells from cord blood	blood
13	chr5:80611600-80623600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr5:80611800-80619000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:80612200-80623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr5:80613000-80613200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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