Variant report

Variant	rs40882
Chromosome Location	chr7:108159220-108159221
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	chr7:108154890..108162900-chr7:108163401..108168908,16	K562	blood:
2	chr7:108150412..108153237-chr7:108158566..108160870,2	K562	blood:

Variant related genes	Relation type
ENSG00000231006	Chromatin interaction
ENSG00000135241	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10487859	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11974559	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11981670	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12666562	0.81[ASN][1000 genomes]
rs13229488	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13307045	0.83[EUR][1000 genomes]
rs13312593	0.83[EUR][1000 genomes]
rs17155828	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17424206	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs194587	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2214914	0.82[EUR][1000 genomes]
rs2214915	0.82[EUR][1000 genomes]
rs3202837	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs33987381	0.83[EUR][1000 genomes]
rs34333829	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34583262	0.83[EUR][1000 genomes]
rs34814097	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34887057	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35372181	0.84[ASN][1000 genomes]
rs35880371	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs40843	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs40845	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs40850	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs40854	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs40872	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40875	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40878	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40880	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40885	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40886	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40895	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40899	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40900	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40901	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40902	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40908	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40910	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40915	0.86[ASN][1000 genomes]
rs40921	0.80[ASN][1000 genomes]
rs40923	0.86[ASN][1000 genomes]
rs40924	0.86[ASN][1000 genomes]
rs40925	0.86[ASN][1000 genomes]
rs40928	0.86[ASN][1000 genomes]
rs40934	0.81[ASN][1000 genomes]
rs40938	0.81[ASN][1000 genomes]
rs40939	0.81[ASN][1000 genomes]
rs40940	0.81[ASN][1000 genomes]
rs40941	0.81[ASN][1000 genomes]
rs40944	0.81[ASN][1000 genomes]
rs40945	0.81[ASN][1000 genomes]
rs40946	0.81[ASN][1000 genomes]
rs40947	0.81[ASN][1000 genomes]
rs41385644	0.83[EUR][1000 genomes]
rs4992578	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60426977	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6466238	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs67694466	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6947492	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6955152	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6967368	0.83[EUR][1000 genomes]
rs71568528	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9785056	0.83[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs40882	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs40882	THAP5	cis	Esophagus Muscularis	GTEx
rs40882	THAP5	cis	Heart Left Ventricle	GTEx
rs40882	THAP5	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 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	chr7:108114400-108160000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr7:108117800-108164200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:108130000-108165000	Weak transcription	Pancreas	Pancrea
7	chr7:108130200-108162000	Weak transcription	Hela-S3	cervix
8	chr7:108130800-108165000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:108136000-108163000	Weak transcription	HepG2	liver
10	chr7:108141400-108165000	Weak transcription	Spleen	Spleen
11	chr7:108142000-108161600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr7:108142800-108159800	Weak transcription	Ovary	ovary
13	chr7:108144400-108162200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr7:108144600-108164000	Weak transcription	Fetal Brain Male	brain
15	chr7:108147600-108164400	Weak transcription	Stomach Mucosa	stomach
16	chr7:108148200-108163000	Weak transcription	Fetal Intestine Small	intestine
17	chr7:108148200-108165000	Weak transcription	Fetal Stomach	stomach
18	chr7:108149400-108165600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr7:108150400-108160400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr7:108150800-108160200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr7:108150800-108162200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:108150800-108162800	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:108152000-108160800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr7:108152400-108163000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:108152400-108163600	Weak transcription	NHDF-Ad	bronchial
26	chr7:108152400-108164200	Weak transcription	HMEC	breast
27	chr7:108153600-108165800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr7:108155000-108161800	Weak transcription	Brain Angular Gyrus	brain
29	chr7:108156000-108163200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr7:108156000-108164600	Weak transcription	HUVEC	blood vessel
31	chr7:108156800-108162600	Strong transcription	Primary B cells from cord blood	blood
32	chr7:108157000-108160000	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:108157000-108160600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr7:108157200-108160600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr7:108157400-108161000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:108157400-108161200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:108157400-108162400	Weak transcription	Psoas Muscle	Psoas
38	chr7:108157600-108160000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr7:108157600-108160400	Strong transcription	Placenta	Placenta
40	chr7:108157600-108161000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr7:108157600-108161200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr7:108157800-108161000	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr7:108157800-108161200	Strong transcription	Liver	Liver
44	chr7:108158000-108159600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr7:108158000-108160600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr7:108158000-108162000	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:108158400-108160000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr7:108158400-108165000	Weak transcription	Lung	lung
49	chr7:108158600-108163400	Weak transcription	Right Ventricle	heart
50	chr7:108158600-108163600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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