Variant report

Variant	rs17705732
Chromosome Location	chr15:52120428-52120429
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HCFC1	chr15:52119891-52124267	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52072025..52074741-chr15:52120265..52123225,4	MCF-7	breast:
2	chr15:52119461..52123475-chr15:52166022..52168353,4	MCF-7	breast:
3	chr15:52118547..52120941-chr15:52173181..52175406,2	K562	blood:

Variant related genes	Relation type
TMOD3	TF binding region
ENSG00000128872	Chromatin interaction
ENSG00000138594	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs1001690	0.81[CHB][hapmap]
rs1025184	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[ASN][1000 genomes]
rs1035739	0.87[ASN][1000 genomes]
rs10444798	0.90[ASN][1000 genomes]
rs10444823	0.95[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs10775145	0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs11630084	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs11632106	0.85[ASN][1000 genomes]
rs11636345	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs11638161	0.90[ASN][1000 genomes]
rs11638766	0.87[ASN][1000 genomes]
rs11638820	0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs12438686	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12903707	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs12905283	0.86[CHB][hapmap];0.89[CHD][hapmap];0.85[ASN][1000 genomes]
rs12917133	0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs1545602	0.90[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs1811326	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1867984	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1895863	0.94[ASN][1000 genomes]
rs1972689	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2009972	0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[ASN][1000 genomes]
rs2034857	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2034858	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2052709	0.90[CHB][hapmap];0.86[ASN][1000 genomes]
rs2241503	0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[ASN][1000 genomes]
rs2252606	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs2253116	0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[ASN][1000 genomes]
rs2264339	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2414119	0.98[ASN][1000 genomes]
rs2436658	0.87[ASN][1000 genomes]
rs2436661	0.99[ASN][1000 genomes]
rs2470602	0.87[ASN][1000 genomes]
rs2470603	0.87[ASN][1000 genomes]
rs2470604	0.83[ASN][1000 genomes]
rs2470605	0.85[ASN][1000 genomes]
rs2470607	0.85[ASN][1000 genomes]
rs2470616	0.81[ASN][1000 genomes]
rs2470617	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs2470619	0.92[ASN][1000 genomes]
rs2554305	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2554306	0.99[ASN][1000 genomes]
rs2554307	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs2554308	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2554315	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2554334	0.94[ASN][1000 genomes]
rs2554336	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2554342	0.88[ASN][1000 genomes]
rs2554345	0.94[ASN][1000 genomes]
rs2554349	0.90[CHB][hapmap];0.98[CHD][hapmap];0.88[ASN][1000 genomes]
rs2554350	0.88[ASN][1000 genomes]
rs2570228	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2570231	0.99[ASN][1000 genomes]
rs2570233	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2570237	0.95[ASN][1000 genomes]
rs2570238	0.92[ASN][1000 genomes]
rs2570258	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2570260	0.94[ASN][1000 genomes]
rs2570263	0.86[ASN][1000 genomes]
rs2570268	0.89[ASN][1000 genomes]
rs2570269	0.87[ASN][1000 genomes]
rs2570271	0.87[ASN][1000 genomes]
rs2570275	0.88[ASN][1000 genomes]
rs2593167	0.82[ASN][1000 genomes]
rs2593173	0.95[CHB][hapmap];0.98[CHD][hapmap];0.89[ASN][1000 genomes]
rs2593179	0.87[ASN][1000 genomes]
rs2593183	0.89[ASN][1000 genomes]
rs2593185	0.90[CHB][hapmap];0.87[ASN][1000 genomes]
rs2593187	0.95[CHB][hapmap];0.87[ASN][1000 genomes]
rs2593191	0.94[ASN][1000 genomes]
rs2593198	0.88[ASN][1000 genomes]
rs2593202	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs2593204	0.87[ASN][1000 genomes]
rs2623254	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2623262	0.94[ASN][1000 genomes]
rs2623279	0.89[ASN][1000 genomes]
rs2623281	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs2623283	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs2623286	0.87[ASN][1000 genomes]
rs2623288	0.89[ASN][1000 genomes]
rs2623289	0.87[ASN][1000 genomes]
rs2959302	0.83[ASN][1000 genomes]
rs3751596	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs3794530	0.86[ASN][1000 genomes]
rs3794534	0.90[CHB][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs3794535	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs3794536	0.98[ASN][1000 genomes]
rs4238383	0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4502160	0.87[ASN][1000 genomes]
rs4534783	0.87[ASN][1000 genomes]
rs4774602	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs4775978	0.90[CHB][hapmap];0.84[JPT][hapmap];0.89[ASN][1000 genomes]
rs4775982	0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs4775983	0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs55843525	0.89[ASN][1000 genomes]
rs58758283	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60329909	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493518	0.87[ASN][1000 genomes]
rs6493519	0.90[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs6493522	0.97[ASN][1000 genomes]
rs6493523	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs689884	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs689922	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs690287	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs690638	0.87[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7162554	0.85[ASN][1000 genomes]
rs7165283	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7166110	0.85[ASN][1000 genomes]
rs7168659	0.81[CHB][hapmap]
rs7171459	0.97[ASN][1000 genomes]
rs7173375	0.85[ASN][1000 genomes]
rs7176421	0.95[ASN][1000 genomes]
rs7181553	0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs72732952	0.94[ASN][1000 genomes]
rs8024081	0.90[ASN][1000 genomes]
rs8024088	0.90[ASN][1000 genomes]
rs8024589	0.90[ASN][1000 genomes]
rs8026521	0.82[ASN][1000 genomes]
rs8028890	0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs8031045	0.82[CHB][hapmap];0.83[GIH][hapmap];0.82[TSI][hapmap]
rs8041268	0.97[ASN][1000 genomes]
rs919059	0.94[ASN][1000 genomes]
rs9635308	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs990665	0.89[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	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17705732	USP8	cis	cerebellum	SCAN
rs17705732	GNB5	cis	Skin Sun Exposed Lower leg	GTEx
rs17705732	MYO5A	cis	cerebellum	SCAN
rs17705732	LEO1	cis	parietal	SCAN
rs17705732	KIAA1370	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52107200-52121400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:52114000-52121200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:52114000-52121400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:52114000-52121600	Weak transcription	Aorta	Aorta
5	chr15:52114200-52121600	Weak transcription	Psoas Muscle	Psoas
6	chr15:52117600-52121600	Weak transcription	NHDF-Ad	bronchial
7	chr15:52117800-52120800	Weak transcription	A549	lung
8	chr15:52118200-52121200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr15:52118400-52121000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:52118800-52121000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:52118800-52121400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr15:52118800-52121400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:52118800-52121600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:52119600-52120600	Enhancers	Hela-S3	cervix
15	chr15:52120000-52120600	Enhancers	Placenta Amnion	Placenta Amnion
16	chr15:52120000-52121000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:52120000-52121400	Weak transcription	Fetal Brain Male	brain
18	chr15:52120400-52121000	Enhancers	K562	blood
19	chr15:52120400-52121000	Enhancers	NHEK	skin
20	chr15:52120400-52121600	Enhancers	HMEC	breast
21	chr15:52120400-52121800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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