Variant report

Variant	rs7172021
Chromosome Location	chr15:73449003-73449004
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	chr15:73426527..73428787-chr15:73446978..73449108,2	MCF-7	breast:
2	chr15:73440487..73443797-chr15:73445568..73450386,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000067141	Chromatin interaction

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs10048053	0.88[ASN][1000 genomes]
rs1023924	0.88[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs1038137	0.81[CHB][hapmap]
rs10438294	0.81[CHD][hapmap]
rs10467948	0.81[CHB][hapmap]
rs10467949	1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs1116880	0.85[AMR][1000 genomes];0.86[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];0.81[ASN][1000 genomes]
rs11634147	0.84[AMR][1000 genomes]
rs11636241	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11639213	0.81[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap]
rs11856922	0.81[ASN][1000 genomes]
rs12050685	0.82[CEU][hapmap];0.87[TSI][hapmap]
rs12050774	0.92[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12050848	0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs12708506	0.82[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12899246	0.83[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs12907139	0.88[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs12916928	0.81[ASN][1000 genomes]
rs13379875	0.81[CHB][hapmap];0.81[GIH][hapmap]
rs1479337	0.80[CHB][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs1479338	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1479339	0.87[CEU][hapmap];0.94[CHB][hapmap];0.87[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1479340	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1564345	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]
rs17762516	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17762600	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]
rs17829830	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17829836	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17829957	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1812835	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1871385	0.86[CHD][hapmap]
rs2010793	0.87[ASN][1000 genomes]
rs2046017	0.89[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs2127277	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2169951	0.81[CHB][hapmap]
rs2251205	0.89[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs2415147	0.81[JPT][hapmap]
rs2415148	0.92[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28481558	0.81[ASN][1000 genomes]
rs28743094	0.81[ASN][1000 genomes]
rs28842482	0.83[ASN][1000 genomes]
rs2899784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35060813	0.81[ASN][1000 genomes]
rs3736510	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs3784793	1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs3784801	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes]
rs3985587	0.84[AMR][1000 genomes]
rs3985588	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4132535	0.83[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4132536	0.80[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap]
rs4545783	0.80[AMR][1000 genomes]
rs4609810	0.81[EUR][1000 genomes]
rs4776630	0.85[ASN][1000 genomes]
rs4777582	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs4777589	0.83[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4777590	0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap]
rs4777591	0.83[CHB][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs4777598	0.84[AMR][1000 genomes]
rs546564	0.84[CEU][hapmap]
rs55646651	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55853625	0.84[AMR][1000 genomes]
rs55868723	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55939596	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56157337	0.90[ASN][1000 genomes]
rs56215298	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56348595	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58060856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59066156	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62015460	0.84[EUR][1000 genomes]
rs62015500	0.85[AMR][1000 genomes]
rs62015502	0.85[AMR][1000 genomes]
rs62016803	0.82[EUR][1000 genomes]
rs62016849	0.80[AMR][1000 genomes]
rs62016851	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62016853	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62016854	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62016856	0.85[EUR][1000 genomes]
rs62016858	0.84[EUR][1000 genomes]
rs62017774	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62017776	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62017779	0.91[ASN][1000 genomes]
rs6416501	0.81[ASN][1000 genomes]
rs6416502	0.81[ASN][1000 genomes]
rs6495047	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7164894	0.83[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7165610	0.81[EUR][1000 genomes]
rs7169083	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7172396	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173142	0.81[ASN][1000 genomes]
rs7175329	0.83[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs74022925	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs74025262	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs747873	0.86[CHD][hapmap]
rs7495458	0.81[ASN][1000 genomes]
rs8026121	0.81[CHB][hapmap]
rs8026579	0.83[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs8027588	0.82[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap]
rs8029106	0.91[ASN][1000 genomes]
rs8035063	0.90[ASN][1000 genomes]
rs8042700	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs922516	0.83[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs9672588	0.80[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs9806496	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920186	0.83[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv527236	chr15:73421239-73469535	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7172021	THAP10	cis	cerebellum	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
2	chr15:73414400-73458200	Weak transcription	Colonic Mucosa	Colon
3	chr15:73416000-73453200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr15:73424200-73449200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:73429000-73456600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr15:73429200-73449200	Weak transcription	Gastric	stomach
7	chr15:73430200-73466600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:73431800-73453800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:73443600-73456600	Weak transcription	Fetal Kidney	kidney
10	chr15:73445600-73457400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:73446400-73450000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:73446800-73449200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
13	chr15:73447200-73470000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:73447600-73457800	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr15:73447600-73457800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:73447800-73458000	Weak transcription	Brain Angular Gyrus	brain
17	chr15:73448000-73457000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr15:73448000-73469000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr15:73448400-73449200	ZNF genes & repeats	Brain Substantia Nigra	brain
20	chr15:73448400-73449800	ZNF genes & repeats	Fetal Stomach	stomach
21	chr15:73448600-73449200	ZNF genes & repeats	Fetal Muscle Leg	muscle
22	chr15:73448600-73449800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:73448600-73449800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:73448600-73449800	ZNF genes & repeats	Lung	lung
25	chr15:73448600-73450000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:73448600-73450000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
27	chr15:73448600-73450000	ZNF genes & repeats	Fetal Intestine Small	intestine
28	chr15:73448600-73455800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr15:73448800-73449200	ZNF genes & repeats	Ovary	ovary
30	chr15:73448800-73450000	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr15:73448800-73450000	Strong transcription	Fetal Intestine Large	intestine
32	chr15:73448800-73454400	Weak transcription	Psoas Muscle	Psoas
33	chr15:73448800-73458000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:73448800-73458000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr15:73449000-73449200	Strong transcription	Brain Hippocampus Middle	brain
36	chr15:73449000-73449400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr15:73449000-73449400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:73449000-73449400	Strong transcription	Brain Anterior Caudate	brain
39	chr15:73449000-73450000	Strong transcription	Fetal Lung	lung
40	chr15:73449000-73451400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:73449000-73454400	Weak transcription	Aorta	Aorta
42	chr15:73449000-73458000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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