Variant report

Variant	rs7620040
Chromosome Location	chr3:134163082-134163083
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10935114	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs12634127	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1498726	0.83[AMR][1000 genomes]
rs3846053	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs3846054	0.86[CHB][hapmap];0.80[JPT][hapmap]
rs4602357	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs7628967	0.80[CHB][hapmap]
rs7650509	0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs9842113	0.92[CEU][hapmap];0.90[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9842140	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv967068	chr3:134153022-134165125	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs7620040	ANAPC13	cis	Esophagus Muscularis	GTEx
rs7620040	ANAPC13	cis	cerebellum	SCAN
rs7620040	CEP63	cis	multi-tissue	Pritchard
rs7620040	ANAPC13	cis	Muscle Skeletal	GTEx
rs7620040	ANAPC13	cis	Artery Tibial	GTEx
rs7620040	ANAPC13	cis	Nerve Tibial	GTEx
rs7620040	CEP63	cis	Skin Sun Exposed Lower leg	GTEx
rs7620040	ANAPC13	cis	Thyroid	GTEx
rs7620040	TXNDC6	cis	cerebellum	SCAN
rs7620040	ANAPC13	cis	parietal	SCAN
rs7620040	ANAPC13	cis	Adipose Subcutaneous	GTEx
rs7620040	ANAPC13	cis	multi-tissue	Pritchard
rs7620040	ANAPC13	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134160400-134164400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr3:134160800-134164400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr3:134160800-134164400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:134161000-134164400	Weak transcription	NHEK	skin
5	chr3:134161200-134163200	Weak transcription	Osteobl	bone
6	chr3:134161200-134163800	Weak transcription	NHDF-Ad	bronchial
7	chr3:134161200-134164400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:134161200-134164400	Weak transcription	Fetal Lung	lung
9	chr3:134161200-134166600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:134161400-134164200	Weak transcription	Adipose Nuclei	Adipose
11	chr3:134161400-134164400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:134161400-134164400	Weak transcription	HMEC	breast
13	chr3:134161600-134164400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:134162400-134163200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:134163000-134166600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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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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