Variant report

Variant	rs12050685
Chromosome Location	chr15:73477482-73477483
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	chr15:73475429..73477756-chr15:73487732..73490810,3	MCF-7	breast:
2	chr15:73475200..73477819-chr15:73479193..73482817,3	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1116880	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11634084	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12050658	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12050774	0.89[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs1479338	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs1479339	0.83[CEU][hapmap];0.88[EUR][1000 genomes]
rs1479340	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs1564345	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs17762146	0.84[ASW][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17762516	0.85[EUR][1000 genomes]
rs17762600	0.89[CEU][hapmap];0.82[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs17829830	0.89[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs17829957	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1812835	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs1964543	0.82[EUR][1000 genomes]
rs1979409	0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2127277	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs2415148	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs2899784	0.84[CEU][hapmap]
rs3784801	0.95[CEU][hapmap]
rs3985588	0.93[EUR][1000 genomes]
rs546564	0.89[CEU][hapmap]
rs55646651	0.88[EUR][1000 genomes]
rs55868723	0.90[EUR][1000 genomes]
rs55916847	0.82[AFR][1000 genomes]
rs55939596	0.87[EUR][1000 genomes]
rs56118677	0.91[AFR][1000 genomes]
rs56215298	0.87[EUR][1000 genomes]
rs56348595	0.87[EUR][1000 genomes]
rs59066156	0.96[EUR][1000 genomes]
rs62015460	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62015484	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62015499	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62015500	0.83[EUR][1000 genomes]
rs62015502	0.82[EUR][1000 genomes]
rs62015504	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62016793	0.91[AFR][1000 genomes]
rs62016808	0.82[EUR][1000 genomes]
rs62016813	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62016850	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs62016851	0.80[EUR][1000 genomes]
rs62016853	0.88[EUR][1000 genomes]
rs62016854	0.87[EUR][1000 genomes]
rs62016856	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62016857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62016858	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62017774	0.87[EUR][1000 genomes]
rs62017776	0.87[EUR][1000 genomes]
rs7169083	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs7172021	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs7172396	0.82[CEU][hapmap]
rs74022925	0.87[EUR][1000 genomes]
rs74025262	0.88[EUR][1000 genomes]
rs7497992	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9806496	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv904339	chr15:73375847-73483718	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	nsv904341	chr15:73390790-73483718	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	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
8	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
rs12050685	THAP10	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
2	chr15:73454600-73483000	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:73455200-73500400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:73458600-73478000	Weak transcription	Colonic Mucosa	Colon
5	chr15:73459000-73482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:73466800-73482000	Weak transcription	Psoas Muscle	Psoas
7	chr15:73468600-73481200	Weak transcription	Lung	lung
8	chr15:73470800-73481600	Weak transcription	Brain Angular Gyrus	brain
9	chr15:73471400-73478600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:73472000-73488400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr15:73472000-73496800	Weak transcription	Ovary	ovary
12	chr15:73472200-73504600	Weak transcription	Left Ventricle	heart
13	chr15:73473400-73496400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:73474200-73478200	Strong transcription	Fetal Intestine Large	intestine
15	chr15:73474200-73479600	Weak transcription	Fetal Kidney	kidney
16	chr15:73474200-73482400	Weak transcription	Gastric	stomach
17	chr15:73474200-73482600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:73474200-73487800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:73474200-73488800	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr15:73474200-73498200	Weak transcription	Liver	Liver
21	chr15:73474200-73523800	Weak transcription	Esophagus	oesophagus
22	chr15:73474400-73477800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr15:73474400-73478000	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:73474400-73481800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:73474600-73478200	Strong transcription	Fetal Lung	lung
26	chr15:73474600-73488000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr15:73474600-73500600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:73474800-73478200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:73475200-73486800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:73475200-73517600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:73475400-73495600	Weak transcription	Brain Anterior Caudate	brain
32	chr15:73475800-73478800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr15:73475800-73481200	Weak transcription	Aorta	Aorta
34	chr15:73475800-73492000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:73476000-73479000	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr15:73476000-73479000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:73476000-73480600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:73476000-73482600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:73476000-73487800	Weak transcription	Pancreas	Pancrea
40	chr15:73476000-73492000	Weak transcription	Fetal Intestine Small	intestine
41	chr15:73476000-73493800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr15:73476000-73494800	Weak transcription	Brain Hippocampus Middle	brain
43	chr15:73476200-73477800	Weak transcription	Fetal Muscle Trunk	muscle
44	chr15:73476200-73478000	Weak transcription	A549	lung
45	chr15:73476200-73487800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr15:73476200-73493800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:73476200-73495000	Weak transcription	Brain Substantia Nigra	brain
48	chr15:73476200-73506200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr15:73476400-73478400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:73476400-73486800	Weak transcription	Rectal Mucosa Donor 29	rectum

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