Variant report

Variant	rs1564345
Chromosome Location	chr15:73497874-73497875
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73493630..73495142-chr15:73497332..73499715,2	K562	blood:
2	chr15:73463612..73466544-chr15:73496830..73498478,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10048053	0.89[ASN][1000 genomes]
rs1023924	0.88[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap]
rs1038137	0.81[CHB][hapmap]
rs10438294	0.81[CHD][hapmap]
rs10467948	0.81[CHB][hapmap]
rs10467949	1.00[CHD][hapmap];0.81[ASN][1000 genomes]
rs1116880	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1131854	0.82[CHB][hapmap];0.91[CHD][hapmap]
rs11632639	0.83[CHB][hapmap];0.85[CHD][hapmap];0.88[JPT][hapmap]
rs11634147	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11636241	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11639213	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12050685	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs12050774	0.92[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12050848	0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs12708506	0.82[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs12899246	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs12907139	0.88[CHB][hapmap];0.93[JPT][hapmap];0.96[ASN][1000 genomes]
rs13379875	0.81[CHB][hapmap]
rs1479337	0.80[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1479338	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1479339	0.87[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1479340	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17762516	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17762600	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17829830	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17829836	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17829957	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1812835	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1871385	0.86[CHD][hapmap]
rs2010793	0.81[ASN][1000 genomes]
rs2046017	0.89[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs2127277	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2169951	0.81[CHB][hapmap]
rs2251205	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2415147	0.81[JPT][hapmap]
rs2415148	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2899784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3736510	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs3784793	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs3784801	0.95[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3985587	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3985588	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4132535	0.83[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs4132536	0.80[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap]
rs4776630	0.87[ASN][1000 genomes]
rs4777582	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs4777589	0.83[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4777590	0.81[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap]
rs4777591	0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs4777598	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs546564	0.84[CEU][hapmap]
rs55646651	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55853625	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55868723	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55939596	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56157337	0.96[ASN][1000 genomes]
rs56215298	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56348595	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58060856	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59066156	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62015460	0.85[EUR][1000 genomes]
rs62015500	0.83[AMR][1000 genomes]
rs62015502	0.83[AMR][1000 genomes]
rs62016803	0.81[EUR][1000 genomes]
rs62016851	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62016853	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62016854	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62016856	0.84[EUR][1000 genomes]
rs62016858	0.83[EUR][1000 genomes]
rs62017774	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62017776	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62017779	0.95[ASN][1000 genomes]
rs6495047	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs7164894	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs7169083	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7172021	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7172396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7175329	0.83[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs74022925	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs74025262	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs747873	0.86[CHD][hapmap]
rs8026121	0.81[CHB][hapmap]
rs8026579	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs8027588	0.82[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap]
rs8029106	0.95[ASN][1000 genomes]
rs8035063	0.96[ASN][1000 genomes]
rs8042700	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs922516	0.83[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs9672588	0.80[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs9806496	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9920186	0.83[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][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	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv904340	chr15:73375847-73524629	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv904342	chr15:73390790-73524629	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1564345	THAP10	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73455200-73500400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:73472200-73504600	Weak transcription	Left Ventricle	heart
3	chr15:73474200-73498200	Weak transcription	Liver	Liver
4	chr15:73474200-73523800	Weak transcription	Esophagus	oesophagus
5	chr15:73474600-73500600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:73475200-73517600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:73476200-73506200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr15:73477600-73503800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr15:73477800-73499200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr15:73482000-73504600	Weak transcription	Aorta	Aorta
11	chr15:73483600-73505800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr15:73487200-73519800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr15:73489000-73502200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:73492200-73518000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:73492400-73516200	Weak transcription	Fetal Brain Male	brain
16	chr15:73493400-73504400	Weak transcription	Fetal Intestine Small	intestine
17	chr15:73493400-73528600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr15:73495000-73499000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:73495600-73502600	Weak transcription	Small Intestine	intestine
20	chr15:73495600-73504600	Weak transcription	Psoas Muscle	Psoas
21	chr15:73495800-73507400	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:73496200-73506200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:73496400-73500000	Strong transcription	Fetal Intestine Large	intestine
24	chr15:73496600-73498200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:73496800-73498000	Strong transcription	Fetal Lung	lung
26	chr15:73496800-73498000	Strong transcription	Ovary	ovary
27	chr15:73496800-73498000	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr15:73496800-73507400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:73497000-73499600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:73497000-73517600	Weak transcription	Brain Hippocampus Middle	brain
31	chr15:73497400-73498000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
32	chr15:73497400-73498000	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr15:73497400-73504400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:73497400-73505800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:73497800-73541800	Weak transcription	Fetal Kidney	kidney

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