Variant report

Variant	rs2190896
Chromosome Location	chr7:108220343-108220344
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:108214879..108218601-chr7:108220209..108223552,3	MCF-7	breast:
2	chr7:108219591..108221299-chr7:108232211..108234837,2	MCF-7	breast:

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10081203	0.91[AFR][1000 genomes]
rs10215273	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10953575	0.91[AFR][1000 genomes]
rs35846666	1.00[EUR][1000 genomes]
rs40917	0.82[YRI][hapmap]
rs4140914	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55645791	1.00[EUR][1000 genomes]
rs56231121	1.00[EUR][1000 genomes]
rs57881876	1.00[EUR][1000 genomes]
rs6943408	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73426189	1.00[EUR][1000 genomes]
rs73426193	1.00[EUR][1000 genomes]
rs73426197	1.00[EUR][1000 genomes]
rs73713110	1.00[EUR][1000 genomes]
rs73713177	1.00[EUR][1000 genomes]
rs73713178	1.00[EUR][1000 genomes]
rs73713180	1.00[EUR][1000 genomes]
rs73713181	1.00[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	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
rs2190896	THAP5	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108212000-108222600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr7:108212400-108221600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr7:108212600-108220400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr7:108213000-108222200	Weak transcription	HMEC	breast
5	chr7:108214400-108222200	Weak transcription	HSMMtube	muscle
6	chr7:108214400-108222600	Weak transcription	Small Intestine	intestine
7	chr7:108214400-108225000	Weak transcription	Fetal Brain Male	brain
8	chr7:108214600-108222200	Weak transcription	Fetal Kidney	kidney
9	chr7:108214800-108220600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr7:108215800-108221600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr7:108216000-108222000	Weak transcription	HepG2	liver
12	chr7:108216200-108223000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:108216200-108224600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:108216400-108222400	Weak transcription	Fetal Heart	heart
15	chr7:108216400-108229400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr7:108216600-108222400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:108216800-108224600	Weak transcription	NHEK	skin
18	chr7:108217000-108222400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr7:108218600-108221600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr7:108219000-108220400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr7:108219000-108221000	ZNF genes & repeats	Dnd41	blood
22	chr7:108219200-108220600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:108219200-108220600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr7:108219200-108220600	Strong transcription	Colon Smooth Muscle	Colon
25	chr7:108219200-108220600	ZNF genes & repeats	Fetal Brain Female	brain
26	chr7:108219200-108220600	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr7:108219200-108220800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr7:108219200-108220800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr7:108219200-108220800	Strong transcription	A549	lung
30	chr7:108219200-108221000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr7:108219200-108221000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr7:108219400-108220400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr7:108219400-108220400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
34	chr7:108219400-108220400	Strong transcription	Primary T helper cells fromperipheralblood	blood
35	chr7:108219400-108220400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:108219400-108220400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr7:108219400-108220400	ZNF genes & repeats	Fetal Thymus	thymus
38	chr7:108219400-108220400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
39	chr7:108219400-108220600	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
40	chr7:108219400-108220600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:108219400-108220600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr7:108219400-108220600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr7:108219400-108220600	ZNF genes & repeats	Brain Anterior Caudate	brain
44	chr7:108219400-108220600	ZNF genes & repeats	Fetal Muscle Trunk	muscle
45	chr7:108219400-108220600	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr7:108219400-108220600	Strong transcription	Stomach Smooth Muscle	stomach
47	chr7:108219400-108220800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr7:108219400-108220800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr7:108219400-108220800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
50	chr7:108219400-108221000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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