Variant report

Variant	rs13097818
Chromosome Location	chr3:134146709-134146710
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:134091888..134095593-chr3:134142304..134147270,4	MCF-7	breast:
2	chr3:134110212..134112141-chr3:134146148..134148218,2	MCF-7	breast:
3	chr3:134146261..134149924-chr3:134150087..134151982,3	MCF-7	breast:
4	chr3:134145112..134147635-chr3:134150719..134152522,2	MCF-7	breast:
5	chr3:134139549..134143630-chr3:134144649..134147393,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114019	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11916983	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11917131	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11917156	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11924801	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13059980	0.80[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13067502	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13067509	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13074369	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13075432	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2241557	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34102849	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35088484	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35394720	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35922016	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35944310	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4312629	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4552325	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4596118	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4602357	0.82[MEX][hapmap]
rs4605513	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4607082	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6767595	0.86[AMR][1000 genomes]
rs6771701	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6796705	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7611834	0.91[MEX][hapmap]
rs7637740	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7644093	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[GIH][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7644251	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7647128	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9789971	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9789972	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9790169	0.83[AMR][1000 genomes]
rs9809989	1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9822766	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9824904	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9829477	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9829637	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9835166	0.86[CHB][hapmap]
rs9839295	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9847750	0.86[MEX][hapmap]
rs9848223	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9851770	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	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
4	nsv1007607	chr3:134131521-134156814	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	7 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs13097818	ANAPC13	cis	lesional skin	skin_eQTL
rs13097818	ANAPC13	cis	Artery Tibial	GTEx
rs13097818	TXNDC6	cis	cerebellum	SCAN
rs13097818	ANAPC13	Cis_1M	lymphoblastoid	RTeQTL
rs13097818	ANAPC13	cis	parietal	SCAN
rs13097818	ANAPC13	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134142000-134148800	Weak transcription	Spleen	Spleen
2	chr3:134142400-134147600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr3:134144800-134148200	Enhancers	Placenta Amnion	Placenta Amnion
4	chr3:134145000-134147800	Enhancers	NH-A	brain
5	chr3:134145000-134148200	Enhancers	NHLF	lung
6	chr3:134145000-134148400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:134145000-134148400	Enhancers	Osteobl	bone
8	chr3:134145200-134147000	Enhancers	HSMMtube	muscle
9	chr3:134145200-134147800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:134145200-134148000	Enhancers	NHDF-Ad	bronchial
11	chr3:134145200-134148200	Enhancers	HSMM	muscle
12	chr3:134145200-134148600	Enhancers	Hela-S3	cervix
13	chr3:134145200-134149200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:134145400-134147800	Enhancers	Placenta	Placenta
15	chr3:134145400-134148400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:134145400-134148400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:134145400-134148600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:134145400-134149600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:134145600-134147800	Enhancers	HMEC	breast
20	chr3:134145600-134148000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:134145800-134147000	Enhancers	Esophagus	oesophagus
22	chr3:134145800-134147000	Enhancers	Fetal Muscle Leg	muscle
23	chr3:134145800-134147000	Flanking Active TSS	A549	lung
24	chr3:134145800-134147000	Enhancers	HUVEC	blood vessel
25	chr3:134145800-134147600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:134146000-134147000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr3:134146000-134147800	Enhancers	Pancreas	Pancrea
28	chr3:134146200-134147000	Enhancers	Gastric	stomach
29	chr3:134146200-134147000	Flanking Active TSS	NHEK	skin
30	chr3:134146200-134147600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:134146200-134148600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr3:134146400-134147600	Weak transcription	Adipose Nuclei	Adipose
33	chr3:134146400-134149200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:134146400-134150400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:134146600-134147600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:134146600-134147600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:134146600-134147600	Enhancers	HepG2	liver
38	chr3:134146600-134148600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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