Variant report

Variant	rs9649308
Chromosome Location	chr7:108096291-108096292
allele	A/G
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	chr7:108094270..108096861-chr7:108164817..108167585,2	MCF-7	breast:
2	chr1:149857130..149858704-chr7:108095136..108097059,2	MCF-7	breast:
3	chr7:108094702..108096715-chr7:108133980..108136057,2	MCF-7	breast:
4	chr7:107996666..108000210-chr7:108094187..108098858,6	MCF-7	breast:
5	chr2:172808708..172810698-chr7:108094975..108096588,2	MCF-7	breast:
6	chr7:108095582..108097658-chr7:108210312..108212186,2	MCF-7	breast:
7	chr7:107817682..107823715-chr7:108094168..108099407,9	MCF-7	breast:
8	chr20:45986504..45989171-chr7:108094917..108096710,2	MCF-7	breast:
9	chr7:108094254..108096481-chr7:108100316..108102970,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000135241	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000128590	Chromatin interaction
ENSG00000091129	Chromatin interaction
ENSG00000266112	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10487859	0.90[EUR][1000 genomes]
rs11973105	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11974559	0.86[EUR][1000 genomes]
rs11981670	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12705470	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13227836	0.87[EUR][1000 genomes]
rs13228190	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13229488	0.90[EUR][1000 genomes]
rs13238841	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13245101	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13245242	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13307045	0.88[EUR][1000 genomes]
rs13312593	0.88[EUR][1000 genomes]
rs17155828	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17338441	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17338462	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17423043	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17423119	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17424206	0.90[EUR][1000 genomes]
rs194587	0.90[EUR][1000 genomes]
rs2214913	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214914	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2214915	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2300048	0.89[EUR][1000 genomes]
rs2300052	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3202837	0.89[EUR][1000 genomes]
rs33987381	0.93[EUR][1000 genomes]
rs34218460	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34333829	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34583262	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34814097	0.89[EUR][1000 genomes]
rs34887057	0.89[EUR][1000 genomes]
rs35436957	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35617326	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35880371	0.84[EUR][1000 genomes]
rs40843	0.90[EUR][1000 genomes]
rs40845	0.90[EUR][1000 genomes]
rs40850	0.90[EUR][1000 genomes]
rs40854	0.86[EUR][1000 genomes]
rs40872	0.85[EUR][1000 genomes]
rs40875	0.87[EUR][1000 genomes]
rs40878	0.87[EUR][1000 genomes]
rs40880	0.84[EUR][1000 genomes]
rs40885	0.85[EUR][1000 genomes]
rs40886	0.84[EUR][1000 genomes]
rs40895	0.85[EUR][1000 genomes]
rs40899	0.85[EUR][1000 genomes]
rs40900	0.85[EUR][1000 genomes]
rs40901	0.85[EUR][1000 genomes]
rs40902	0.84[EUR][1000 genomes]
rs40908	0.85[EUR][1000 genomes]
rs40910	0.83[EUR][1000 genomes]
rs41385644	0.93[EUR][1000 genomes]
rs4992578	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56145857	0.88[EUR][1000 genomes]
rs59458537	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60398019	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60426977	0.88[EUR][1000 genomes]
rs6466233	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6466238	0.87[EUR][1000 genomes]
rs66461825	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67027479	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67694466	0.88[EUR][1000 genomes]
rs6947492	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6949637	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6955152	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6959023	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6967368	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6976309	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6976649	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6976659	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6976752	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6976776	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6976804	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6978552	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs71213282	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7784170	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7786947	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7790875	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7806869	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7807737	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7807941	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7811808	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9649307	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9785056	0.93[EUR][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	esv3358442	chr7:108095941-108098489	Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9649308	THAP5	cis	Esophagus Muscularis	GTEx
rs9649308	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108094600-108097800	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr7:108094800-108096800	Active TSS	Brain Angular Gyrus	brain
3	chr7:108094800-108096800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
4	chr7:108094800-108097800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:108095000-108096400	Bivalent/Poised TSS	Thymus	Thymus
6	chr7:108095000-108096600	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
7	chr7:108095000-108096600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
8	chr7:108095000-108096800	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
9	chr7:108095000-108096800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
10	chr7:108095000-108096800	Bivalent/Poised TSS	NHDF-Ad	bronchial
11	chr7:108095000-108097000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr7:108095000-108097000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr7:108095000-108097200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr7:108095000-108097200	Active TSS	HSMM	muscle
15	chr7:108095000-108097400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:108095000-108097400	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr7:108095000-108097400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr7:108095000-108097400	Active TSS	A549	lung
19	chr7:108095000-108097600	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr7:108095000-108097600	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr7:108095000-108097800	Active TSS	Fetal Brain Female	brain
22	chr7:108095000-108098000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
23	chr7:108095200-108096400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
24	chr7:108095200-108096600	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr7:108095200-108096800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:108095200-108096800	Flanking Active TSS	Liver	Liver
27	chr7:108095200-108096800	Active TSS	Brain Substantia Nigra	brain
28	chr7:108095200-108096800	Active TSS	Fetal Brain Male	brain
29	chr7:108095200-108096800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
30	chr7:108095200-108097000	Active TSS	HSMMtube	muscle
31	chr7:108095200-108097000	Bivalent/Poised TSS	NHLF	lung
32	chr7:108095200-108097200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr7:108095200-108097200	Active TSS	Aorta	Aorta
34	chr7:108095200-108097200	Active TSS	Fetal Kidney	kidney
35	chr7:108095200-108097200	Active TSS	HUVEC	blood vessel
36	chr7:108095200-108097200	Bivalent/Poised TSS	Osteobl	bone
37	chr7:108095200-108097400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr7:108095200-108097600	Active TSS	H9 Cell Line	embryonic stem cell
39	chr7:108095200-108097600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
40	chr7:108095200-108097600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
41	chr7:108095200-108097600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
42	chr7:108095200-108097600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr7:108095200-108097800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr7:108095200-108097800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
45	chr7:108095200-108097800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:108095200-108097800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
47	chr7:108095200-108098000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr7:108095200-108098200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
49	chr7:108095400-108096600	Bivalent/Poised TSS	Brain Germinal Matrix	brain
50	chr7:108095400-108096600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain

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