Variant report

Variant	rs2041003
Chromosome Location	chr7:108213166-108213167
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:108199426-108221976	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:107786172..107787859-chr7:108212708..108215561,2	MCF-7	breast:
2	chr7:108163122..108173185-chr7:108207236..108216619,40	K562	blood:
3	chr7:108159403..108171484-chr7:108200740..108214365,45	K562	blood:
4	chr7:108213141..108217464-chr7:108225107..108230596,8	K562	blood:
5	chr7:108162967..108170259-chr7:108208242..108216228,25	MCF-7	breast:
6	chr7:108209600..108213665-chr7:112090307..112092525,3	K562	blood:

No data

Variant related genes	Relation type
THAP5	TF binding region
PNPLA8	TF binding region
ENSG00000135241	Chromatin interaction
ENSG00000006652	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10156002	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253210	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10270723	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10282368	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1043615	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17426315	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072212	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34668718	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs40911	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs40913	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40916	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs40918	0.85[EUR][1000 genomes]
rs40922	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40927	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40929	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40930	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40933	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs40937	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40943	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730324	0.91[ASN][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	nsv817371	chr7:108199882-108649799	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2041003	THAP5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108207400-108213400	Active TSS	GM12878-XiMat	blood
2	chr7:108209400-108213200	Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr7:108211200-108214200	Weak transcription	Small Intestine	intestine
4	chr7:108211200-108219400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:108211200-108219600	Weak transcription	Lung	lung
6	chr7:108211400-108213400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr7:108211400-108215400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr7:108211400-108216600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:108211400-108217400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr7:108211400-108219400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:108211400-108219600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:108211400-108219600	Weak transcription	Colonic Mucosa	Colon
13	chr7:108211400-108219600	Weak transcription	Esophagus	oesophagus
14	chr7:108211400-108219600	Weak transcription	Ovary	ovary
15	chr7:108211400-108219800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr7:108211600-108213400	Weak transcription	Fetal Muscle Leg	muscle
17	chr7:108211600-108213600	Weak transcription	HSMMtube	muscle
18	chr7:108211600-108214400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:108211600-108215800	Weak transcription	Thymus	Thymus
20	chr7:108211600-108219200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:108211600-108219200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr7:108211600-108219400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:108211600-108219400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr7:108211600-108220000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr7:108211800-108213200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr7:108211800-108213200	Weak transcription	Placenta	Placenta
27	chr7:108211800-108213400	Weak transcription	Fetal Thymus	thymus
28	chr7:108211800-108214600	Weak transcription	Stomach Mucosa	stomach
29	chr7:108211800-108218400	Weak transcription	NHLF	lung
30	chr7:108211800-108219800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr7:108212000-108213200	Weak transcription	Osteobl	bone
32	chr7:108212000-108213400	Weak transcription	A549	lung
33	chr7:108212000-108213400	Weak transcription	NHDF-Ad	bronchial
34	chr7:108212000-108214800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr7:108212000-108219400	Weak transcription	Brain Germinal Matrix	brain
36	chr7:108212000-108219600	Weak transcription	Fetal Stomach	stomach
37	chr7:108212000-108222600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr7:108212200-108213600	Enhancers	Fetal Brain Male	brain
39	chr7:108212200-108214800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr7:108212200-108219400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr7:108212200-108219600	Weak transcription	Brain Hippocampus Middle	brain
42	chr7:108212200-108219800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr7:108212400-108213200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr7:108212400-108213200	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr7:108212400-108213200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr7:108212400-108213200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr7:108212400-108213400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr7:108212400-108213400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr7:108212400-108213400	Weak transcription	Brain Substantia Nigra	brain
50	chr7:108212400-108213400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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