Variant report

Variant	rs10245718
Chromosome Location	chr7:108055631-108055632
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	chr7:108054248..108057900-chr7:108068091..108071582,3	MCF-7	breast:
2	chr7:108006500..108008005-chr7:108054331..108056945,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11976021	0.86[CEU][hapmap]
rs11979596	0.87[CEU][hapmap];0.81[AMR][1000 genomes]
rs12669879	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs12705470	0.82[AMR][1000 genomes]
rs13227836	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs13228190	0.84[AMR][1000 genomes]
rs13238841	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs13245101	0.82[AMR][1000 genomes]
rs13245242	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs17155637	0.86[CEU][hapmap]
rs17338441	0.84[AMR][1000 genomes]
rs17338462	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs17421351	0.86[CEU][hapmap]
rs17423043	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs17423119	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs2108253	0.85[CEU][hapmap]
rs2300036	0.81[CEU][hapmap]
rs2300048	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs2300052	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs35436957	0.82[AMR][1000 genomes]
rs59458537	0.81[AMR][1000 genomes]
rs60398019	0.81[AMR][1000 genomes]
rs6466224	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs6466225	0.82[CEU][hapmap]
rs6466226	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs6466233	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs6954366	0.82[AMR][1000 genomes]
rs6959409	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs6960478	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs6966107	0.91[CEU][hapmap];0.82[AMR][1000 genomes]
rs6969521	0.87[CEU][hapmap];0.82[AMR][1000 genomes]
rs6978552	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs7784170	0.83[CEU][hapmap];0.82[AMR][1000 genomes]
rs7786947	0.83[CEU][hapmap]
rs7790875	0.82[CEU][hapmap];0.82[AMR][1000 genomes]
rs7806869	0.83[CEU][hapmap];0.81[AMR][1000 genomes]
rs7807737	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10245718	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs10245718	THAP5	cis	normal skin	skin_eQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108049400-108056400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr7:108050000-108056400	Weak transcription	Fetal Brain Female	brain
3	chr7:108053800-108056400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr7:108054000-108056400	Enhancers	HSMMtube	muscle
5	chr7:108054200-108055800	Enhancers	HMEC	breast
6	chr7:108054200-108056000	Enhancers	Primary hematopoietic stem cells	blood
7	chr7:108054200-108056200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr7:108054200-108056400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr7:108054200-108056400	Enhancers	Primary B cells from peripheral blood	blood
10	chr7:108054200-108056600	Enhancers	Brain Angular Gyrus	brain
11	chr7:108054200-108056800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:108054200-108057000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:108054200-108057000	Enhancers	Fetal Muscle Leg	muscle
14	chr7:108054200-108057600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:108054200-108057600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:108054200-108057600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr7:108054200-108057600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr7:108054200-108057800	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr7:108054200-108058600	Enhancers	Brain Anterior Caudate	brain
20	chr7:108054200-108058800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr7:108054200-108059200	Enhancers	HUVEC	blood vessel
22	chr7:108054400-108055800	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr7:108054400-108055800	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr7:108054400-108056400	Enhancers	GM12878-XiMat	blood
25	chr7:108054400-108056600	Enhancers	Primary B cells from cord blood	blood
26	chr7:108054600-108056200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr7:108054600-108056400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr7:108054600-108056400	Enhancers	HSMM	muscle
29	chr7:108054600-108056600	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr7:108054600-108056600	Weak transcription	NHDF-Ad	bronchial
31	chr7:108054600-108057600	Enhancers	Brain Cingulate Gyrus	brain
32	chr7:108054800-108056200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:108054800-108056400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:108054800-108056600	Weak transcription	Osteobl	bone
35	chr7:108054800-108061000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr7:108055000-108055800	Enhancers	Pancreas	Pancrea
37	chr7:108055000-108056400	Weak transcription	NH-A	brain
38	chr7:108055000-108062600	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr7:108055200-108056200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr7:108055200-108056200	Weak transcription	NHEK	skin
41	chr7:108055200-108056400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr7:108055200-108056400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr7:108055200-108056600	Enhancers	Fetal Muscle Trunk	muscle
44	chr7:108055200-108057800	Enhancers	Fetal Brain Male	brain
45	chr7:108055400-108055800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr7:108055400-108056200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr7:108055400-108056400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr7:108055400-108056400	Weak transcription	Brain Substantia Nigra	brain
49	chr7:108055400-108056400	Enhancers	A549	lung
50	chr7:108055400-108056600	Weak transcription	Brain Hippocampus Middle	brain

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