Variant report

Variant	rs40878
Chromosome Location	chr7:108157011-108157012
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108143447..108146507-chr7:108154602..108157266,3	MCF-7	breast:
2	chr7:108155135..108157387-chr7:108160534..108162897,2	K562	blood:
3	chr7:108155944..108157453-chr7:108161889..108164868,2	MCF-7	breast:
4	chr7:108154890..108162900-chr7:108163401..108168908,16	K562	blood:
5	chr7:108152047..108154125-chr7:108156232..108158415,2	K562	blood:

Variant related genes	Relation type
ENSG00000135241	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10487859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11973105	0.86[EUR][1000 genomes]
rs11974559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12666562	0.86[ASN][1000 genomes]
rs12705470	0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs13227836	0.83[EUR][1000 genomes]
rs13228190	0.84[EUR][1000 genomes]
rs13229488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13238841	0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs13245101	0.86[EUR][1000 genomes]
rs13245242	0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs13307045	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13312593	0.91[EUR][1000 genomes]
rs17155828	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17338441	0.86[EUR][1000 genomes]
rs17338462	0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs17423043	0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs17423119	0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs17424206	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs194587	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214913	0.86[EUR][1000 genomes]
rs2214914	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2214915	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2300048	0.84[EUR][1000 genomes]
rs2300052	0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs3202837	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33987381	0.92[EUR][1000 genomes]
rs34218460	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34333829	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34583262	0.92[EUR][1000 genomes]
rs34814097	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34887057	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35372181	0.88[ASN][1000 genomes]
rs35436957	0.84[EUR][1000 genomes]
rs35617326	0.86[EUR][1000 genomes]
rs35880371	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3763457	0.83[ASN][1000 genomes]
rs40843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40850	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40854	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40875	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40880	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40882	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40885	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40895	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40899	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40901	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40915	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40921	0.84[ASN][1000 genomes]
rs40923	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40924	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40925	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40928	0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs40934	0.86[ASN][1000 genomes]
rs40938	0.86[ASN][1000 genomes]
rs40939	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40940	0.86[ASN][1000 genomes]
rs40941	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs40944	0.86[ASN][1000 genomes]
rs40945	0.86[ASN][1000 genomes]
rs40946	0.86[ASN][1000 genomes]
rs40947	0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs41385644	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4992578	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56145857	0.83[EUR][1000 genomes]
rs59458537	0.84[EUR][1000 genomes]
rs60398019	0.83[EUR][1000 genomes]
rs60426977	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6466233	0.84[EUR][1000 genomes]
rs6466238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66461825	0.86[EUR][1000 genomes]
rs67027479	0.86[EUR][1000 genomes]
rs67694466	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6947492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6949637	0.86[EUR][1000 genomes]
rs6955152	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6959023	0.85[EUR][1000 genomes]
rs6967368	0.91[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6976309	0.86[EUR][1000 genomes]
rs6976649	0.85[EUR][1000 genomes]
rs6976659	0.86[EUR][1000 genomes]
rs6976752	0.86[EUR][1000 genomes]
rs6976776	0.86[EUR][1000 genomes]
rs6976804	0.86[EUR][1000 genomes]
rs6978552	0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs71213282	0.86[EUR][1000 genomes]
rs71568528	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784170	0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs7786947	0.89[JPT][hapmap];0.86[EUR][1000 genomes]
rs7790875	0.89[JPT][hapmap];0.84[EUR][1000 genomes]
rs7806869	0.84[EUR][1000 genomes]
rs7807737	0.86[EUR][1000 genomes]
rs7807941	0.86[EUR][1000 genomes]
rs7811808	0.87[EUR][1000 genomes]
rs9649307	0.86[EUR][1000 genomes]
rs9649308	0.87[EUR][1000 genomes]
rs9785056	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs40878	THAP5	cis	multi-tissue	Pritchard
rs40878	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs40878	THAP5	cis	Esophagus Muscularis	GTEx
rs40878	THAP5	cis	Muscle Skeletal	GTEx
rs40878	THAP5	cis	Heart Left Ventricle	GTEx
rs40878	THAP5	cis	uninvolved skin	skin_eQTL
rs40878	THAP5	cis	normal skin	skin_eQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108102800-108158400	Weak transcription	HSMMtube	muscle
2	chr7:108105800-108158000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr7:108109000-108162400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr7:108113800-108165800	Weak transcription	Gastric	stomach
5	chr7:108114000-108165000	Weak transcription	Colonic Mucosa	Colon
6	chr7:108114400-108160000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr7:108117800-108164200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr7:108119200-108157600	Weak transcription	Brain Germinal Matrix	brain
9	chr7:108119800-108158200	Weak transcription	Aorta	Aorta
10	chr7:108121600-108158200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr7:108128200-108158000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr7:108130000-108165000	Weak transcription	Pancreas	Pancrea
13	chr7:108130200-108162000	Weak transcription	Hela-S3	cervix
14	chr7:108130800-108165000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr7:108132800-108158400	Weak transcription	A549	lung
16	chr7:108135200-108158000	Weak transcription	Right Ventricle	heart
17	chr7:108136000-108163000	Weak transcription	HepG2	liver
18	chr7:108137200-108158200	Weak transcription	NH-A	brain
19	chr7:108140600-108157600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr7:108140800-108157600	Weak transcription	Brain Substantia Nigra	brain
21	chr7:108141200-108158200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr7:108141400-108165000	Weak transcription	Spleen	Spleen
23	chr7:108142000-108161600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr7:108142200-108158000	Weak transcription	Esophagus	oesophagus
25	chr7:108142200-108158200	Weak transcription	Lung	lung
26	chr7:108142800-108159800	Weak transcription	Ovary	ovary
27	chr7:108143000-108158000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:108144400-108162200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr7:108144600-108158000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr7:108144600-108158000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr7:108144600-108164000	Weak transcription	Fetal Brain Male	brain
32	chr7:108147600-108164400	Weak transcription	Stomach Mucosa	stomach
33	chr7:108148200-108163000	Weak transcription	Fetal Intestine Small	intestine
34	chr7:108148200-108165000	Weak transcription	Fetal Stomach	stomach
35	chr7:108149400-108165600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr7:108150400-108160400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr7:108150600-108159000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr7:108150800-108160200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr7:108150800-108162200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr7:108150800-108162800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr7:108151000-108157800	Weak transcription	Colon Smooth Muscle	Colon
42	chr7:108152000-108160800	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr7:108152200-108158200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr7:108152200-108158400	Weak transcription	GM12878-XiMat	blood
45	chr7:108152400-108158400	Weak transcription	Brain Hippocampus Middle	brain
46	chr7:108152400-108163000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr7:108152400-108163600	Weak transcription	NHDF-Ad	bronchial
48	chr7:108152400-108164200	Weak transcription	HMEC	breast
49	chr7:108152600-108158000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr7:108152600-108158000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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