Variant report

Variant	rs5023563
Chromosome Location	chr2:34455549-34455550
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10180100	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10187841	0.82[EUR][1000 genomes]
rs10865096	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11124366	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11687656	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11889234	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12611702	0.90[EUR][1000 genomes]
rs13407683	0.93[ASN][1000 genomes]
rs1862064	0.96[ASN][1000 genomes]
rs2005906	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2112018	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2193808	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216491	0.96[ASN][1000 genomes]
rs2371922	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4417695	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5023562	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6543816	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6719456	0.88[EUR][1000 genomes]
rs6729467	0.82[EUR][1000 genomes]
rs6733379	0.93[ASN][1000 genomes]
rs6757428	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7569103	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7569181	0.81[EUR][1000 genomes]
rs7574426	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584555	0.89[EUR][1000 genomes]
rs7586688	0.89[ASN][1000 genomes]
rs918328	0.96[ASN][1000 genomes]
rs972053	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006001	chr2:33991364-34858721	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv535628	chr2:33991364-34858721	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv873799	chr2:33996983-34821990	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv999091	chr2:34154486-34993188	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv535629	chr2:34154486-34993188	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv873804	chr2:34156867-35047107	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
7	nsv873808	chr2:34275757-34703057	Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1012401	chr2:34302403-34468097	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv833714	chr2:34348193-34504892	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs5023563	FAM82A1	cis	cerebellum	SCAN
rs5023563	TTC27	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:34455400-34456400	Weak transcription	Ovary	ovary
2	chr2:34455400-34460200	Weak transcription	Pancreas	Pancrea

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