Variant report

Variant	rs1479340
Chromosome Location	chr15:73472887-73472888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73472565..73474187-chr15:73479031..73481328,2	K562	blood:

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10048053	0.89[ASN][1000 genomes]
rs1023924	0.88[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.81[AMR][1000 genomes]
rs1038137	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10438294	0.81[CHD][hapmap]
rs10467948	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10467949	1.00[CHD][hapmap];0.84[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];0.83[JPT][hapmap]
rs11634147	0.84[AMR][1000 genomes]
rs11636241	0.82[CHB][hapmap]
rs11639213	0.81[CEU][hapmap];0.82[CHB][hapmap]
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];0.94[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12050848	0.88[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs12708506	0.82[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs12899246	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs12902768	0.81[JPT][hapmap]
rs12907139	0.88[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs13379875	0.81[CHB][hapmap];0.81[GIH][hapmap]
rs1479337	0.80[CHB][hapmap];0.84[ASN][1000 genomes]
rs1479338	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1479339	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1564345	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	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17762600	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]
rs17829830	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17829836	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17829957	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[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];0.81[JPT][hapmap]
rs2010793	0.84[ASN][1000 genomes]
rs2046017	0.89[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs2127277	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169951	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2251205	0.89[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs2415147	0.87[JPT][hapmap]
rs2415148	0.92[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28842482	0.81[ASN][1000 genomes]
rs2899784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736510	0.86[CHD][hapmap];0.87[JPT][hapmap]
rs3784793	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[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]
rs4132536	0.80[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs4545783	0.80[AMR][1000 genomes]
rs4609810	0.81[EUR][1000 genomes]
rs4776630	0.87[ASN][1000 genomes]
rs4777582	0.83[CHB][hapmap]
rs4777589	0.83[CHB][hapmap];1.00[CHD][hapmap];0.84[ASN][1000 genomes]
rs4777590	0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs4777591	0.83[CHB][hapmap];0.85[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	0.93[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[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	0.92[ASN][1000 genomes]
rs6495047	0.83[CHB][hapmap]
rs7164894	0.83[CHB][hapmap]
rs7165610	0.81[EUR][1000 genomes]
rs7169083	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7172021	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]
rs7172396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7175329	0.83[CHB][hapmap];1.00[CHD][hapmap];0.85[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]
rs747872	0.81[JPT][hapmap]
rs747873	0.86[CHD][hapmap];0.81[JPT][hapmap]
rs8026121	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs8026579	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs8027588	0.82[CHB][hapmap];0.94[CHD][hapmap]
rs8029106	0.92[ASN][1000 genomes]
rs8035063	0.93[ASN][1000 genomes]
rs8042700	0.81[CEU][hapmap];0.87[JPT][hapmap]
rs922516	0.83[CHB][hapmap];1.00[CHD][hapmap]
rs9672588	0.80[CEU][hapmap];0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs9806496	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9920186	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs9972523	0.80[ASN][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
rs1479340	THAP10	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73401400-73480200	Weak transcription	Right Ventricle	heart
2	chr15:73450000-73475400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:73450000-73477400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr15:73454600-73483000	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:73455000-73473800	Weak transcription	Fetal Stomach	stomach
6	chr15:73455200-73500400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:73458600-73473200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr15:73458600-73478000	Weak transcription	Colonic Mucosa	Colon
9	chr15:73459000-73482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:73459200-73473800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:73459200-73473800	Weak transcription	Fetal Intestine Small	intestine
12	chr15:73459400-73473400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:73462400-73473800	Weak transcription	Fetal Brain Female	brain
14	chr15:73466200-73473800	Weak transcription	Esophagus	oesophagus
15	chr15:73466800-73473800	Weak transcription	Fetal Muscle Leg	muscle
16	chr15:73466800-73482000	Weak transcription	Psoas Muscle	Psoas
17	chr15:73467000-73473800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:73467000-73473800	Weak transcription	Aorta	Aorta
19	chr15:73467000-73473800	Weak transcription	Gastric	stomach
20	chr15:73467200-73473800	Weak transcription	Pancreas	Pancrea
21	chr15:73467400-73473600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:73467600-73473200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:73467600-73473800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:73467800-73475200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr15:73467800-73476800	Weak transcription	Fetal Brain Male	brain
26	chr15:73468000-73475400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr15:73468200-73473600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:73468200-73473800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr15:73468200-73475000	Weak transcription	Brain Substantia Nigra	brain
30	chr15:73468400-73475000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:73468400-73475600	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:73468600-73476200	Weak transcription	Small Intestine	intestine
33	chr15:73468600-73481200	Weak transcription	Lung	lung
34	chr15:73468800-73475400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr15:73469000-73473200	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:73469000-73473600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:73469000-73474400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:73469200-73473200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:73469600-73475000	Weak transcription	Brain Anterior Caudate	brain
40	chr15:73470000-73473600	Strong transcription	Liver	Liver
41	chr15:73470000-73476400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr15:73470400-73477200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:73470800-73477400	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:73470800-73481600	Weak transcription	Brain Angular Gyrus	brain
45	chr15:73471000-73473400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr15:73471000-73473600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:73471400-73478600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:73472000-73473200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr15:73472000-73473400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:73472000-73473400	Weak transcription	Duodenum Mucosa	Duodenum

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