Variant report

Variant	rs2140671
Chromosome Location	chr10:54745248-54745249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10824848	0.94[EUR][1000 genomes]
rs10824853	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11003294	0.96[EUR][1000 genomes]
rs11003295	0.96[EUR][1000 genomes]
rs11003303	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1343051	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1343052	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1343070	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1539512	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880396	0.97[EUR][1000 genomes]
rs1880397	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1917162	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1917165	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1917166	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1917171	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1935936	0.91[ASN][1000 genomes]
rs1949816	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2066436	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2244530	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2244637	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2244778	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2248899	0.88[ASN][1000 genomes]
rs2249349	0.87[ASN][1000 genomes]
rs2249356	0.87[ASN][1000 genomes]
rs2253123	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2384100	0.83[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2462480	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2488606	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2492355	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4935055	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7095436	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7902771	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv831877	chr10:54565135-54764638	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	nsv508584	chr10:54704765-54747382	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	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
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2140671	RP11-319F12.2	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54734600-54764600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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