Variant report

Variant	rs12666562
Chromosome Location	chr7:108219099-108219100
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	chr7:108217454..108219397-chr7:108235662..108238254,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10487859	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs11974559	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];0.86[ASN][1000 genomes]
rs11981670	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs13229488	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs17155828	0.81[ASN][1000 genomes]
rs17424206	0.81[ASN][1000 genomes]
rs194587	0.81[ASN][1000 genomes]
rs3202837	0.81[ASN][1000 genomes]
rs34814097	0.81[ASN][1000 genomes]
rs34887057	0.81[ASN][1000 genomes]
rs35372181	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35880371	0.81[ASN][1000 genomes]
rs3763457	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs40843	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs40845	0.90[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs40850	0.81[ASN][1000 genomes]
rs40854	0.81[ASN][1000 genomes]
rs40872	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40875	0.86[ASN][1000 genomes]
rs40878	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40880	0.86[ASN][1000 genomes]
rs40882	0.81[ASN][1000 genomes]
rs40885	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40886	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs40895	0.86[ASN][1000 genomes]
rs40899	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40900	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40901	0.86[ASN][1000 genomes]
rs40902	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40908	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40910	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40912	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs40914	0.86[EUR][1000 genomes]
rs40915	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40919	0.92[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs40921	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs40923	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40924	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40925	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40926	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs40928	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40931	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs40932	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs40934	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40936	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs40938	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40939	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40940	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40941	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40942	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.87[EUR][1000 genomes]
rs40944	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40945	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40946	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40947	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40948	0.87[EUR][1000 genomes]
rs60426977	0.81[ASN][1000 genomes]
rs6466238	0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs67694466	0.81[ASN][1000 genomes]
rs6947492	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6955152	0.81[ASN][1000 genomes]
rs71568528	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12666562	THAP5	cis	uninvolved skin	skin_eQTL
rs12666562	THAP5	cis	normal skin	skin_eQTL
rs12666562	THAP5	cis	multi-tissue	Pritchard
rs12666562	THAP5	cis	lymphoblastoid	seeQTL
rs12666562	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108211200-108219400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:108211200-108219600	Weak transcription	Lung	lung
3	chr7:108211400-108219400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:108211400-108219600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:108211400-108219600	Weak transcription	Colonic Mucosa	Colon
6	chr7:108211400-108219600	Weak transcription	Esophagus	oesophagus
7	chr7:108211400-108219600	Weak transcription	Ovary	ovary
8	chr7:108211400-108219800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr7:108211600-108219200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr7:108211600-108219200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr7:108211600-108219400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr7:108211600-108219400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr7:108211600-108220000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:108211800-108219800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr7:108212000-108219400	Weak transcription	Brain Germinal Matrix	brain
16	chr7:108212000-108219600	Weak transcription	Fetal Stomach	stomach
17	chr7:108212000-108222600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:108212200-108219400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr7:108212200-108219600	Weak transcription	Brain Hippocampus Middle	brain
20	chr7:108212200-108219800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr7:108212400-108219200	Weak transcription	Fetal Brain Female	brain
22	chr7:108212400-108219400	Weak transcription	Aorta	Aorta
23	chr7:108212400-108219400	Weak transcription	Brain Anterior Caudate	brain
24	chr7:108212400-108219400	Weak transcription	Fetal Intestine Small	intestine
25	chr7:108212400-108219400	Weak transcription	Gastric	stomach
26	chr7:108212400-108219400	Weak transcription	Right Ventricle	heart
27	chr7:108212400-108219600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:108212400-108219600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr7:108212400-108219800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr7:108212400-108220000	Weak transcription	Right Atrium	heart
31	chr7:108212400-108220200	Weak transcription	Psoas Muscle	Psoas
32	chr7:108212400-108221600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr7:108212600-108219400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr7:108212600-108219400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr7:108212600-108220400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr7:108213000-108222200	Weak transcription	HMEC	breast
37	chr7:108214000-108219600	Weak transcription	Brain Substantia Nigra	brain
38	chr7:108214200-108219200	Weak transcription	Colon Smooth Muscle	Colon
39	chr7:108214400-108219400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr7:108214400-108219800	Weak transcription	Fetal Lung	lung
41	chr7:108214400-108222200	Weak transcription	HSMMtube	muscle
42	chr7:108214400-108222600	Weak transcription	Small Intestine	intestine
43	chr7:108214400-108225000	Weak transcription	Fetal Brain Male	brain
44	chr7:108214600-108219400	Strong transcription	Liver	Liver
45	chr7:108214600-108219600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr7:108214600-108222200	Weak transcription	Fetal Kidney	kidney
47	chr7:108214800-108219600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr7:108214800-108219600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr7:108214800-108219600	Weak transcription	Brain Angular Gyrus	brain
50	chr7:108214800-108219600	Weak transcription	Brain Cingulate Gyrus	brain

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