Variant report

Variant	rs40886
Chromosome Location	chr7:108161291-108161292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108159403..108171484-chr7:108200740..108214365,45	K562	blood:
2	chr7:108160741..108162427-chr7:108209446..108212408,2	MCF-7	breast:
3	chr7:108155135..108157387-chr7:108160534..108162897,2	K562	blood:
4	chr7:108154890..108162900-chr7:108163401..108168908,16	K562	blood:

Variant related genes	Relation type
ENSG00000128590	Chromatin interaction
ENSG00000135241	Chromatin interaction
ENSG00000177683	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];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11973105	0.83[EUR][1000 genomes]
rs11974559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12666562	0.86[ASN][1000 genomes]
rs12705470	0.84[JPT][hapmap];0.83[EUR][1000 genomes]
rs13227836	0.80[EUR][1000 genomes]
rs13228190	0.82[EUR][1000 genomes]
rs13229488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13238841	0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs13245101	0.83[EUR][1000 genomes]
rs13245242	0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs13307045	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13312593	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17155828	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17338441	0.83[EUR][1000 genomes]
rs17338462	0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs17423043	0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs17423119	0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs17424206	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs194587	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214913	0.83[EUR][1000 genomes]
rs2214914	0.88[EUR][1000 genomes]
rs2214915	0.88[EUR][1000 genomes]
rs2300048	0.82[EUR][1000 genomes]
rs2300052	0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs3202837	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33987381	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34218460	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34333829	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34583262	0.91[EUR][1000 genomes]
rs34814097	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34887057	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35372181	0.88[ASN][1000 genomes]
rs35436957	0.82[EUR][1000 genomes]
rs35617326	0.83[EUR][1000 genomes]
rs35880371	0.96[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];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40850	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40854	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40872	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40875	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40878	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]
rs40880	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40882	0.86[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];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40895	0.88[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];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40901	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40902	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40915	0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs40921	0.84[ASN][1000 genomes]
rs40923	0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs40924	0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs40925	0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs40928	0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs40934	0.86[ASN][1000 genomes]
rs40938	0.86[ASN][1000 genomes]
rs40939	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs40940	0.86[ASN][1000 genomes]
rs40941	0.88[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	0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs41385644	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4992578	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56145857	0.81[EUR][1000 genomes]
rs59458537	0.81[EUR][1000 genomes]
rs60398019	0.80[EUR][1000 genomes]
rs60426977	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6466233	0.82[EUR][1000 genomes]
rs6466238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66461825	0.83[EUR][1000 genomes]
rs67027479	0.83[EUR][1000 genomes]
rs67694466	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6947492	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6949637	0.83[EUR][1000 genomes]
rs6955152	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6959023	0.83[EUR][1000 genomes]
rs6967368	0.91[CEU][hapmap];0.88[JPT][hapmap];0.89[EUR][1000 genomes]
rs6976309	0.83[EUR][1000 genomes]
rs6976649	0.83[EUR][1000 genomes]
rs6976659	0.83[EUR][1000 genomes]
rs6976752	0.83[EUR][1000 genomes]
rs6976776	0.83[EUR][1000 genomes]
rs6976804	0.83[EUR][1000 genomes]
rs6978552	0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs71213282	0.83[EUR][1000 genomes]
rs71568528	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784170	0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs7786947	0.88[JPT][hapmap];0.83[EUR][1000 genomes]
rs7790875	0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs7806869	0.81[EUR][1000 genomes]
rs7807737	0.83[EUR][1000 genomes]
rs7807941	0.83[EUR][1000 genomes]
rs7811808	0.85[EUR][1000 genomes]
rs9649307	0.83[EUR][1000 genomes]
rs9649308	0.84[EUR][1000 genomes]
rs9785056	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[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
rs40886	THAP5	cis	Esophagus Muscularis	GTEx
rs40886	THAP5	cis	Heart Left Ventricle	GTEx
rs40886	THAP5	cis	uninvolved skin	skin_eQTL
rs40886	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs40886	THAP5	cis	multi-tissue	Pritchard
rs40886	THAP5	cis	normal skin	skin_eQTL
rs40886	THAP5	cis	Muscle Skeletal	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108109000-108162400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:108113800-108165800	Weak transcription	Gastric	stomach
3	chr7:108114000-108165000	Weak transcription	Colonic Mucosa	Colon
4	chr7:108117800-108164200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr7:108130000-108165000	Weak transcription	Pancreas	Pancrea
6	chr7:108130200-108162000	Weak transcription	Hela-S3	cervix
7	chr7:108130800-108165000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:108136000-108163000	Weak transcription	HepG2	liver
9	chr7:108141400-108165000	Weak transcription	Spleen	Spleen
10	chr7:108142000-108161600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr7:108144400-108162200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr7:108144600-108164000	Weak transcription	Fetal Brain Male	brain
13	chr7:108147600-108164400	Weak transcription	Stomach Mucosa	stomach
14	chr7:108148200-108163000	Weak transcription	Fetal Intestine Small	intestine
15	chr7:108148200-108165000	Weak transcription	Fetal Stomach	stomach
16	chr7:108149400-108165600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr7:108150800-108162200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr7:108150800-108162800	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr7:108152400-108163000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:108152400-108163600	Weak transcription	NHDF-Ad	bronchial
21	chr7:108152400-108164200	Weak transcription	HMEC	breast
22	chr7:108153600-108165800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:108155000-108161800	Weak transcription	Brain Angular Gyrus	brain
24	chr7:108156000-108163200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr7:108156000-108164600	Weak transcription	HUVEC	blood vessel
26	chr7:108156800-108162600	Strong transcription	Primary B cells from cord blood	blood
27	chr7:108157400-108162400	Weak transcription	Psoas Muscle	Psoas
28	chr7:108158000-108162000	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr7:108158400-108165000	Weak transcription	Lung	lung
30	chr7:108158600-108163400	Weak transcription	Right Ventricle	heart
31	chr7:108158600-108163600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr7:108158600-108163800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr7:108158600-108164600	Weak transcription	HSMM	muscle
34	chr7:108158600-108164800	Weak transcription	A549	lung
35	chr7:108158600-108165000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr7:108158800-108161600	Weak transcription	Brain Hippocampus Middle	brain
37	chr7:108158800-108161800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr7:108158800-108162000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr7:108158800-108162000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr7:108158800-108162200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr7:108158800-108163600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr7:108158800-108163600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr7:108158800-108163600	Weak transcription	NH-A	brain
44	chr7:108158800-108163800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr7:108158800-108163800	Weak transcription	Fetal Muscle Leg	muscle
46	chr7:108158800-108164000	Weak transcription	Osteobl	bone
47	chr7:108158800-108164200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr7:108158800-108164200	Weak transcription	Esophagus	oesophagus
49	chr7:108158800-108164200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr7:108158800-108164400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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