Variant report

Variant	rs9853860
Chromosome Location	chr3:134310457-134310458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11927540	0.83[AFR][1000 genomes]
rs13322305	0.80[EUR][1000 genomes]
rs2056603	0.88[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs2056604	0.80[EUR][1000 genomes]
rs4535271	0.83[AFR][1000 genomes]
rs6808670	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7433991	0.80[EUR][1000 genomes]
rs7611611	0.80[EUR][1000 genomes]
rs9756173	0.82[EUR][1000 genomes]
rs9851441	0.80[EUR][1000 genomes]
rs9864346	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877510	chr3:134126150-134400448	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv877511	chr3:134174071-134358947	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv877512	chr3:134174071-134372486	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv877513	chr3:134174071-134379752	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv877514	chr3:134191938-134372486	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv829730	chr3:134199097-134359544	Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	nsv1002382	chr3:134239191-134358001	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs9853860	ANAPC13	cis	Esophagus Muscularis	GTEx
rs9853860	CEP63	cis	Esophagus Muscularis	GTEx
rs9853860	CEP63	cis	Skin Sun Exposed Lower leg	GTEx
rs9853860	ANAPC13	cis	Muscle Skeletal	GTEx
rs9853860	CEP63	cis	Artery Tibial	GTEx
rs9853860	ANAPC13	cis	Artery Tibial	GTEx
rs9853860	ANAPC13	cis	Nerve Tibial	GTEx
rs9853860	ANAPC13	cis	Esophagus Mucosa	GTEx
rs9853860	CEP63	cis	Muscle Skeletal	GTEx
rs9853860	CEP63	Cis_1M	lymphoblastoid	RTeQTL
rs9853860	ANAPC13	cis	Stomach	GTEx
rs9853860	ANAPC13	cis	lung	GTEx
rs9853860	ANAPC13	cis	Heart Left Ventricle	GTEx
rs9853860	ANAPC13	cis	Adipose Subcutaneous	GTEx
rs9853860	CEP63	cis	Esophagus Mucosa	GTEx
rs9853860	ANAPC13	cis	Thyroid	GTEx
rs9853860	ANAPC13	cis	Skin Sun Exposed Lower leg	GTEx
rs9853860	ANAPC13	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134309400-134310600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr3:134310000-134314200	Weak transcription	Primary hematopoietic stem cells	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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