Variant report

Variant	rs17762600
Chromosome Location	chr15:73488753-73488754
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73470429..73472525-chr15:73486517..73489040,2	K562	blood:
2	chr15:73475429..73477756-chr15:73487732..73490810,3	MCF-7	breast:

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1023924	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[MKK][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1038137	0.94[CHB][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs10438294	0.81[CHB][hapmap];0.94[CHD][hapmap];0.80[JPT][hapmap]
rs10467948	0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs10467949	0.86[CHD][hapmap]
rs11072403	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11072406	0.94[ASN][1000 genomes]
rs1116880	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11634084	0.82[EUR][1000 genomes]
rs11634147	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12050658	0.88[EUR][1000 genomes]
rs12050685	0.89[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs12050774	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12050848	0.82[JPT][hapmap]
rs12708506	0.82[JPT][hapmap]
rs12902768	0.88[CHB][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs12907139	0.80[JPT][hapmap]
rs13379875	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs1479338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1479339	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1479340	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1564345	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]
rs17762516	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17829830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17829836	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17829957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1812835	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1871385	0.88[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs1979409	0.84[TSI][hapmap]
rs2046017	0.86[CHD][hapmap]
rs2127277	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2169951	0.94[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2251205	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs2415147	0.88[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs2415148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2899784	0.92[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34013312	0.85[ASN][1000 genomes]
rs35450875	0.89[ASN][1000 genomes]
rs3736510	0.88[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3743489	0.87[CHB][hapmap]
rs3784793	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs3784801	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3985587	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3985588	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4132535	0.83[CHD][hapmap]
rs4132536	0.93[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap]
rs4375637	0.80[CHB][hapmap]
rs4545783	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4777589	0.86[CHD][hapmap]
rs4777590	0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs4777598	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs488156	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs498005	0.84[MEX][hapmap];0.81[TSI][hapmap]
rs546564	0.92[CEU][hapmap]
rs55646651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55836604	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55853625	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55868723	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55925663	0.84[ASN][1000 genomes]
rs55939596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56215298	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56269104	0.83[ASN][1000 genomes]
rs56348595	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56377702	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58060856	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59066156	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62015460	0.92[EUR][1000 genomes]
rs62015484	0.85[EUR][1000 genomes]
rs62015499	0.84[EUR][1000 genomes]
rs62015500	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62015502	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62015504	0.82[EUR][1000 genomes]
rs62016806	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62016809	0.82[ASN][1000 genomes]
rs62016811	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62016814	0.82[ASN][1000 genomes]
rs62016849	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62016851	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62016853	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62016854	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62016856	0.94[EUR][1000 genomes]
rs62016857	0.88[EUR][1000 genomes]
rs62016858	0.93[EUR][1000 genomes]
rs62017774	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62017776	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7169083	0.85[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7172021	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7172396	0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7175329	0.86[CHD][hapmap]
rs74022925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74025262	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs747872	0.88[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs747873	0.87[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs7497992	0.88[EUR][1000 genomes]
rs8024575	0.94[ASN][1000 genomes]
rs8026121	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs8035925	0.85[ASN][1000 genomes]
rs8042700	0.82[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs922516	0.86[CHD][hapmap]
rs9806496	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9920186	0.83[CHD][hapmap]
rs9972347	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
rs17762600	THAP10	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73455200-73500400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:73472000-73496800	Weak transcription	Ovary	ovary
3	chr15:73472200-73504600	Weak transcription	Left Ventricle	heart
4	chr15:73473400-73496400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:73474200-73488800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr15:73474200-73498200	Weak transcription	Liver	Liver
7	chr15:73474200-73523800	Weak transcription	Esophagus	oesophagus
8	chr15:73474600-73500600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:73475200-73517600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:73475400-73495600	Weak transcription	Brain Anterior Caudate	brain
11	chr15:73475800-73492000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:73476000-73492000	Weak transcription	Fetal Intestine Small	intestine
13	chr15:73476000-73493800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr15:73476000-73494800	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:73476200-73493800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:73476200-73495000	Weak transcription	Brain Substantia Nigra	brain
17	chr15:73476200-73506200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr15:73477200-73492800	Weak transcription	Fetal Stomach	stomach
19	chr15:73477200-73497400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:73477600-73492000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:73477600-73503800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr15:73477800-73489000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:73477800-73491400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:73477800-73499200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:73478000-73491800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:73478400-73491400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:73478600-73491400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr15:73482000-73492600	Weak transcription	Fetal Intestine Large	intestine
29	chr15:73482000-73504600	Weak transcription	Aorta	Aorta
30	chr15:73483000-73493800	Weak transcription	Adipose Nuclei	Adipose
31	chr15:73483400-73489000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:73483600-73505800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:73483800-73494800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:73485800-73488800	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr15:73486800-73493800	Weak transcription	Fetal Brain Female	brain
36	chr15:73487200-73519800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr15:73488200-73489000	Enhancers	Fetal Brain Male	brain
38	chr15:73488200-73489000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr15:73488200-73494800	Weak transcription	Psoas Muscle	Psoas
40	chr15:73488400-73488800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr15:73488400-73489000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:73488400-73489200	Enhancers	K562	blood
43	chr15:73488400-73489400	Enhancers	Stomach Mucosa	stomach
44	chr15:73488600-73489000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr15:73488600-73489200	Enhancers	Fetal Lung	lung

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