Variant report

Variant	rs10458776
Chromosome Location	chr10:45694706-45694707
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10430732	0.99[EUR][1000 genomes]
rs10430733	0.99[EUR][1000 genomes]
rs10458777	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10508892	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10732899	0.99[EUR][1000 genomes]
rs10751379	0.95[EUR][1000 genomes]
rs10793592	0.98[EUR][1000 genomes]
rs10793593	0.99[EUR][1000 genomes]
rs10793595	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10793596	0.99[EUR][1000 genomes]
rs10793598	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10793599	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10793600	0.97[EUR][1000 genomes]
rs10793601	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793602	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10793603	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10900174	0.96[EUR][1000 genomes]
rs10900175	0.96[EUR][1000 genomes]
rs10900176	0.90[EUR][1000 genomes]
rs10900178	0.99[EUR][1000 genomes]
rs10900179	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10900182	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10900183	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11239374	0.99[EUR][1000 genomes]
rs11239375	0.99[EUR][1000 genomes]
rs11239387	0.94[EUR][1000 genomes]
rs11239390	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12269344	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1856592	0.98[EUR][1000 genomes]
rs2153331	0.99[EUR][1000 genomes]
rs2275847	0.94[EUR][1000 genomes]
rs2282351	0.99[EUR][1000 genomes]
rs2311316	0.97[EUR][1000 genomes]
rs2311317	0.97[EUR][1000 genomes]
rs3851263	0.96[EUR][1000 genomes]
rs4948658	0.99[EUR][1000 genomes]
rs4948953	0.98[EUR][1000 genomes]
rs4948954	0.98[EUR][1000 genomes]
rs4948955	0.99[EUR][1000 genomes]
rs4948959	0.90[EUR][1000 genomes]
rs4948961	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948962	0.98[EUR][1000 genomes]
rs6593462	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6593463	0.99[EUR][1000 genomes]
rs7074910	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7079140	0.97[EUR][1000 genomes]
rs7081346	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7081946	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7094007	0.88[EUR][1000 genomes]
rs7898356	0.89[EUR][1000 genomes]
rs7910939	0.96[EUR][1000 genomes]
rs7911066	0.97[EUR][1000 genomes]
rs7917831	0.99[EUR][1000 genomes]
rs7918108	0.99[EUR][1000 genomes]
rs9326532	0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2750897	chr10:45550145-45820136	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
2	nsv895104	chr10:45636867-45715369	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv895105	chr10:45636867-45928822	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv895106	chr10:45659032-45715369	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv430166	chr10:45668894-46148794	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv947907	chr10:45682432-45695000	Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10458776	AGAP4	cis	Whole Blood	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45694000-45694800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:45694000-45695000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr10:45694200-45694800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr10:45694200-45695000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr10:45694400-45694800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
6	chr10:45694400-45694800	Enhancers	Placenta	Placenta
7	chr10:45694400-45694800	Enhancers	Pancreas	Pancrea
8	chr10:45694400-45694800	Bivalent Enhancer	Right Ventricle	heart
9	chr10:45694400-45695000	ZNF genes & repeats	Lung	lung
10	chr10:45694600-45694800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr10:45694600-45694800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
12	chr10:45694600-45694800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
13	chr10:45694600-45695000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr10:45694600-45695000	Enhancers	Esophagus	oesophagus
15	chr10:45694600-45695000	Enhancers	Gastric	stomach

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