Variant report

Variant	rs7623580
Chromosome Location	chr3:134164345-134164346
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:134049310..134051236-chr3:134163425..134166310,2	MCF-7	breast:
2	chr3:134164113..134166557-chr3:134169956..134171871,3	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11916983	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11917131	0.91[ASN][1000 genomes]
rs11917156	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11924801	0.85[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs12695612	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695613	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13059980	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13066038	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13067502	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13067509	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs13074369	0.91[ASN][1000 genomes]
rs13075432	0.89[ASN][1000 genomes]
rs13097818	0.86[CHB][hapmap]
rs1366067	0.82[AMR][1000 genomes]
rs2241557	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34102849	0.91[ASN][1000 genomes]
rs35088484	0.91[ASN][1000 genomes]
rs35394720	0.91[ASN][1000 genomes]
rs35922016	0.91[ASN][1000 genomes]
rs35944310	0.91[ASN][1000 genomes]
rs4312629	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4552325	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4596118	0.91[ASN][1000 genomes]
rs4605513	0.91[ASN][1000 genomes]
rs4607082	0.91[ASN][1000 genomes]
rs6771701	0.91[ASN][1000 genomes]
rs6791295	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6796705	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7637740	0.86[CHB][hapmap]
rs7644093	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7644251	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7647128	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9789971	0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9789972	0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9809989	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9822766	0.91[ASN][1000 genomes]
rs9826589	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9829477	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9829637	0.86[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9835166	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839295	0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9848223	0.88[ASN][1000 genomes]
rs9851770	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857134	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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
rs7623580	ANAPC13	cis	multi-tissue	Pritchard
rs7623580	ANAPC13	cis	Nerve Tibial	GTEx
rs7623580	ANAPC13	cis	parietal	SCAN
rs7623580	KY	cis	cerebellum	SCAN
rs7623580	CEP63	cis	multi-tissue	Pritchard
rs7623580	ANAPC13	cis	lung	GTEx
rs7623580	ANAPC13	cis	cerebellum	SCAN
rs7623580	ANAPC13	Cis_1M	lymphoblastoid	RTeQTL
rs7623580	CEP63	Cis_1M	lymphoblastoid	RTeQTL
rs7623580	TXNDC6	cis	cerebellum	SCAN
rs7623580	ANAPC13	cis	Artery Tibial	GTEx
rs7623580	ANAPC13	cis	Esophagus Muscularis	GTEx
rs7623580	ANAPC13	cis	Muscle Skeletal	GTEx

Chromatin state (count:24 , 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	chr3:134161200-134164400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:134161200-134164400	Weak transcription	Fetal Lung	lung
7	chr3:134161200-134166600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr3:134161400-134164400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:134161400-134164400	Weak transcription	HMEC	breast
10	chr3:134161600-134164400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:134163000-134166600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:134163200-134164400	Enhancers	Osteobl	bone
13	chr3:134163400-134164600	Weak transcription	Placenta	Placenta
14	chr3:134163400-134164600	Weak transcription	Left Ventricle	heart
15	chr3:134163600-134165800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:134163800-134166800	Enhancers	NHDF-Ad	bronchial
17	chr3:134164000-134164800	Enhancers	Liver	Liver
18	chr3:134164000-134166600	Enhancers	Muscle Satellite Cultured Cells	--
19	chr3:134164200-134164800	Enhancers	Brain Angular Gyrus	brain
20	chr3:134164200-134166400	Enhancers	NH-A	brain
21	chr3:134164200-134166600	Enhancers	HUVEC	blood vessel
22	chr3:134164200-134166600	Enhancers	NHLF	lung
23	chr3:134164200-134167000	Enhancers	Adipose Nuclei	Adipose
24	chr3:134164200-134167200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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