Variant report

Variant	rs17108728
Chromosome Location	chr14:39475193-39475194
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	chr14:39469466..39471750-chr14:39473985..39476478,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10134230	0.87[AMR][1000 genomes]
rs10134654	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10137988	1.00[ASW][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10140341	0.88[ASN][1000 genomes]
rs10140949	0.87[AMR][1000 genomes]
rs10141255	0.87[AMR][1000 genomes]
rs10141471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10148623	0.82[EUR][1000 genomes]
rs10151683	0.84[CHB][hapmap]
rs1061583	1.00[ASW][hapmap]
rs11157041	0.89[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.82[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12050319	0.87[AMR][1000 genomes]
rs12147991	1.00[ASW][hapmap]
rs12434847	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12437031	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12437346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12878139	0.87[AMR][1000 genomes]
rs12878789	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12879229	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12882868	0.87[AMR][1000 genomes]
rs12883061	0.89[ASN][1000 genomes]
rs12885242	1.00[ASW][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12890771	1.00[ASW][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1555257	0.81[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs17108846	1.00[ASW][hapmap]
rs17677562	0.82[EUR][1000 genomes]
rs1957064	0.87[AMR][1000 genomes]
rs2003740	0.83[EUR][1000 genomes]
rs2415522	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2415524	0.90[ASN][1000 genomes]
rs28367031	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28502115	0.90[ASN][1000 genomes]
rs28699217	0.84[ASN][1000 genomes]
rs28810420	0.90[ASN][1000 genomes]
rs34676226	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34702834	0.81[EUR][1000 genomes]
rs34875314	0.83[EUR][1000 genomes]
rs34985331	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35287240	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35423721	0.90[ASN][1000 genomes]
rs35712728	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35807641	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35992529	0.90[ASN][1000 genomes]
rs36161173	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3742354	1.00[ASW][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs3742355	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4899137	0.83[EUR][1000 genomes]
rs4902259	0.81[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4902285	0.82[EUR][1000 genomes]
rs4902308	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902418	1.00[ASW][hapmap]
rs6571893	0.90[ASN][1000 genomes]
rs71407775	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7150092	0.87[AMR][1000 genomes]
rs7151246	0.87[AMR][1000 genomes]
rs7152746	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8018842	0.82[EUR][1000 genomes]
rs8019028	0.82[EUR][1000 genomes]
rs9322992	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9743575	0.87[AMR][1000 genomes]
rs975521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3429206	chr14:39160730-39648836	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1038622	chr14:39423562-39604035	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv564417	chr14:39452317-39535560	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17108728	TRAPPC6B	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39462200-39480400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr14:39463600-39476000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr14:39463600-39495200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr14:39464200-39483000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr14:39464800-39492600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr14:39465600-39498200	Weak transcription	NH-A	brain
7	chr14:39466000-39481000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr14:39466000-39483000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr14:39469200-39497400	Weak transcription	HSMM	muscle
10	chr14:39473400-39498800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr14:39473600-39476400	Enhancers	Fetal Lung	lung
12	chr14:39473800-39476400	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr14:39473800-39485400	Weak transcription	HSMMtube	muscle
14	chr14:39474000-39476600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr14:39474000-39482800	Weak transcription	Right Atrium	heart
16	chr14:39474400-39475200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr14:39474800-39477800	Weak transcription	Lung	lung
18	chr14:39474800-39482600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr14:39475000-39476000	Weak transcription	Placenta	Placenta
20	chr14:39475000-39476200	Weak transcription	Left Ventricle	heart
21	chr14:39475000-39482600	Weak transcription	Right Ventricle	heart
22	chr14:39475000-39485600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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