Variant report

Variant	rs40895
Chromosome Location	chr7:108165515-108165516
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:108163432..108166048-chr7:108192942..108195517,2	K562	blood:
2	chr7:108139312..108141712-chr7:108164785..108166455,2	K562	blood:
3	chr7:108159403..108171484-chr7:108200740..108214365,45	K562	blood:
4	chr7:108094270..108096861-chr7:108164817..108167585,2	MCF-7	breast:
5	chr7:108163986..108165918-chr7:108175176..108176794,2	MCF-7	breast:
6	chr7:108164038..108167949-chr7:108208349..108211666,8	MCF-7	breast:
7	chr7:108162967..108170259-chr7:108208242..108216228,25	MCF-7	breast:
8	chr7:108163136..108166047-chr7:108214620..108217426,3	K562	blood:
9	chr7:108163122..108173185-chr7:108207236..108216619,40	K562	blood:

No data

Variant related genes	Relation type
ENSG00000128590	Chromatin interaction
ENSG00000135241	Chromatin interaction
ENSG00000091129	Chromatin interaction
ENSG00000177683	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10487859	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11973105	0.84[EUR][1000 genomes]
rs11974559	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11981670	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12666562	0.86[ASN][1000 genomes]
rs12705470	0.84[EUR][1000 genomes]
rs13227836	0.81[EUR][1000 genomes]
rs13228190	0.83[EUR][1000 genomes]
rs13229488	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13238841	0.83[EUR][1000 genomes]
rs13245101	0.84[EUR][1000 genomes]
rs13245242	0.84[EUR][1000 genomes]
rs13307045	0.90[EUR][1000 genomes]
rs13312593	0.90[EUR][1000 genomes]
rs17155828	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17338441	0.84[EUR][1000 genomes]
rs17338462	0.84[EUR][1000 genomes]
rs17423043	0.84[EUR][1000 genomes]
rs17423119	0.84[EUR][1000 genomes]
rs17424206	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs194587	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214913	0.84[EUR][1000 genomes]
rs2214914	0.89[EUR][1000 genomes]
rs2214915	0.90[EUR][1000 genomes]
rs2300048	0.83[EUR][1000 genomes]
rs2300052	0.84[EUR][1000 genomes]
rs3202837	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs33987381	0.91[EUR][1000 genomes]
rs34218460	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34333829	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34583262	0.91[EUR][1000 genomes]
rs34814097	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34887057	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35372181	0.88[ASN][1000 genomes]
rs35436957	0.83[EUR][1000 genomes]
rs35617326	0.84[EUR][1000 genomes]
rs35880371	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3763457	0.83[ASN][1000 genomes]
rs40843	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40845	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40850	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40854	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40872	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40875	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40878	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40880	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40882	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40885	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40886	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40899	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40900	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40901	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40902	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40908	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40910	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40915	0.90[ASN][1000 genomes]
rs40921	0.84[ASN][1000 genomes]
rs40923	0.90[ASN][1000 genomes]
rs40924	0.90[ASN][1000 genomes]
rs40925	0.90[ASN][1000 genomes]
rs40928	0.90[ASN][1000 genomes]
rs40934	0.86[ASN][1000 genomes]
rs40938	0.86[ASN][1000 genomes]
rs40939	0.86[ASN][1000 genomes]
rs40940	0.86[ASN][1000 genomes]
rs40941	0.86[ASN][1000 genomes]
rs40944	0.86[ASN][1000 genomes]
rs40945	0.86[ASN][1000 genomes]
rs40946	0.86[ASN][1000 genomes]
rs40947	0.86[ASN][1000 genomes]
rs41385644	0.91[EUR][1000 genomes]
rs4992578	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56145857	0.82[EUR][1000 genomes]
rs59458537	0.83[EUR][1000 genomes]
rs60398019	0.81[EUR][1000 genomes]
rs60426977	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6466233	0.83[EUR][1000 genomes]
rs6466238	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66461825	0.84[EUR][1000 genomes]
rs67027479	0.84[EUR][1000 genomes]
rs67694466	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6947492	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6949637	0.84[EUR][1000 genomes]
rs6955152	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6959023	0.84[EUR][1000 genomes]
rs6967368	0.90[EUR][1000 genomes]
rs6976309	0.84[EUR][1000 genomes]
rs6976649	0.84[EUR][1000 genomes]
rs6976659	0.84[EUR][1000 genomes]
rs6976752	0.84[EUR][1000 genomes]
rs6976776	0.84[EUR][1000 genomes]
rs6976804	0.84[EUR][1000 genomes]
rs6978552	0.83[EUR][1000 genomes]
rs71213282	0.84[EUR][1000 genomes]
rs71568528	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7784170	0.83[EUR][1000 genomes]
rs7786947	0.84[EUR][1000 genomes]
rs7790875	0.83[EUR][1000 genomes]
rs7806869	0.83[EUR][1000 genomes]
rs7807737	0.84[EUR][1000 genomes]
rs7807941	0.84[EUR][1000 genomes]
rs7811808	0.86[EUR][1000 genomes]
rs9649307	0.84[EUR][1000 genomes]
rs9649308	0.85[EUR][1000 genomes]
rs9785056	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs40895	THAP5	cis	uninvolved skin	skin_eQTL
rs40895	THAP5	cis	multi-tissue	Pritchard
rs40895	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs40895	THAP5	cis	normal skin	skin_eQTL
rs40895	THAP5	cis	Heart Left Ventricle	GTEx
rs40895	THAP5	cis	Esophagus Muscularis	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108113800-108165800	Weak transcription	Gastric	stomach
2	chr7:108149400-108165600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:108153600-108165800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:108158800-108165600	Weak transcription	Aorta	Aorta
5	chr7:108160600-108165600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr7:108162000-108165800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr7:108162400-108165800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:108162600-108165600	Enhancers	Primary T cells fromperipheralblood	blood
9	chr7:108162800-108165600	Enhancers	Primary T cells from cord blood	blood
10	chr7:108163000-108165600	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr7:108163000-108165600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr7:108163000-108165600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr7:108163000-108165600	Enhancers	Fetal Intestine Small	intestine
14	chr7:108163400-108166000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr7:108163600-108165800	Weak transcription	Ovary	ovary
16	chr7:108163600-108166000	Flanking Active TSS	Brain Anterior Caudate	brain
17	chr7:108163800-108165600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:108163800-108165600	Enhancers	Fetal Muscle Leg	muscle
19	chr7:108163800-108167400	Active TSS	Brain Cingulate Gyrus	brain
20	chr7:108164000-108165600	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr7:108164000-108165600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:108164000-108165600	Enhancers	Fetal Heart	heart
23	chr7:108164000-108165600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr7:108164200-108165600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr7:108164200-108166800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr7:108164400-108165600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:108164400-108165600	Enhancers	Rectal Smooth Muscle	rectum
28	chr7:108164400-108165600	Enhancers	Thymus	Thymus
29	chr7:108164400-108166000	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr7:108164400-108166400	Active TSS	Right Atrium	heart
31	chr7:108164600-108165600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr7:108164600-108165600	Enhancers	Fetal Thymus	thymus
33	chr7:108164600-108165800	Flanking Active TSS	Hela-S3	cervix
34	chr7:108164600-108166200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr7:108164600-108167800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:108164800-108165600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr7:108164800-108165600	Flanking Active TSS	Brain Germinal Matrix	brain
38	chr7:108164800-108165600	Enhancers	Esophagus	oesophagus
39	chr7:108164800-108165800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
40	chr7:108164800-108166000	Flanking Active TSS	Dnd41	blood
41	chr7:108164800-108167200	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr7:108164800-108167200	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr7:108164800-108167600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr7:108164800-108167600	Active TSS	NHLF	lung
45	chr7:108164800-108167800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr7:108164800-108167800	Active TSS	HUES6 Cell Line	embryonic stem cell
47	chr7:108165000-108165600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr7:108165000-108165600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr7:108165000-108165600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr7:108165000-108165600	Enhancers	Colonic Mucosa	Colon

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