Variant report

Variant	rs11920006
Chromosome Location	chr3:100217983-100217984
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100210709..100213692-chr3:100216752..100220547,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181458	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11923942	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11926280	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11927516	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12636805	0.94[ASN][1000 genomes]
rs12639465	0.81[JPT][hapmap]
rs4132537	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4928097	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4928098	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58059387	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59299896	0.96[ASN][1000 genomes]
rs59771628	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60071944	0.96[ASN][1000 genomes]
rs62276520	0.96[ASN][1000 genomes]
rs62276521	0.96[ASN][1000 genomes]
rs62276522	0.92[ASN][1000 genomes]
rs62276523	0.92[ASN][1000 genomes]
rs62276526	0.88[ASN][1000 genomes]
rs62276527	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6441285	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6441300	0.82[JPT][hapmap]
rs6763079	0.94[CHB][hapmap];0.82[JPT][hapmap];0.96[ASN][1000 genomes]
rs6763178	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs67774605	0.96[ASN][1000 genomes]
rs6789867	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73152126	0.90[ASN][1000 genomes]
rs7430698	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7430715	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs7616839	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7619507	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7630198	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640470	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7653196	0.82[JPT][hapmap]
rs9813069	0.84[ASN][1000 genomes]
rs9851429	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877218	chr3:100176360-100267619	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11920006	TMEM45A	cis	multi-tissue	Pritchard
rs11920006	TMEM45A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100212400-100219200	Weak transcription	Aorta	Aorta
2	chr3:100212400-100222800	Weak transcription	Ovary	ovary
3	chr3:100212800-100224800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr3:100214000-100223600	Weak transcription	Fetal Lung	lung
5	chr3:100214600-100219400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:100215400-100218600	Weak transcription	Liver	Liver
7	chr3:100215800-100219400	Weak transcription	Osteobl	bone
8	chr3:100216000-100218600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:100216200-100218400	Weak transcription	HSMM	muscle
10	chr3:100216200-100219200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:100216200-100219200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:100216200-100219200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr3:100216200-100224400	Weak transcription	HSMMtube	muscle
14	chr3:100216200-100225400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:100216200-100229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:100216400-100218600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:100216400-100219400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr3:100216400-100219400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr3:100217400-100224800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:100217600-100218600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:100217800-100220000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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