Variant report

Variant	rs2462480
Chromosome Location	chr10:54774628-54774629
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10824853	0.89[ASN][1000 genomes]
rs11003303	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1343051	0.87[ASN][1000 genomes]
rs1343052	0.89[ASN][1000 genomes]
rs1343070	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1539512	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1880397	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917162	0.89[ASN][1000 genomes]
rs1917165	0.86[ASN][1000 genomes]
rs1917166	0.86[ASN][1000 genomes]
rs1917171	0.84[ASN][1000 genomes]
rs1935936	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1949816	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2066436	0.94[ASN][1000 genomes]
rs2140671	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2244530	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2244637	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2244778	0.94[ASN][1000 genomes]
rs2248899	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2249349	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249356	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2253123	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488606	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2492355	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4935055	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7095436	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895404	chr10:54545590-54850707	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1043809	chr10:54645158-54860817	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv540627	chr10:54645158-54860817	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv467201	chr10:54697623-54929003	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv550906	chr10:54697623-54929003	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv470939	chr10:54700783-54917339	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv467202	chr10:54735164-54830687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv550907	chr10:54735164-54830687	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	esv1826571	chr10:54765608-54788821	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv895405	chr10:54765608-54824741	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv508585	chr10:54769376-54796804	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2462480	RP11-319F12.2	cis	Thyroid	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54765200-54782600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr10:54767600-54782200	Weak transcription	Fetal Kidney	kidney
3	chr10:54771600-54774800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr10:54773400-54781200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr10:54773600-54782200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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