Variant report

Variant	rs1295993
Chromosome Location	chr3:111590059-111590060
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:111577297..111579661-chr3:111589564..111591815,2	MCF-7	breast:
2	chr3:111589933..111591550-chr3:111593680..111595184,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144824	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16858490	1.00[CEU][hapmap]
rs16858901	1.00[CEU][hapmap]
rs6770127	1.00[CEU][hapmap]
rs6787297	1.00[CEU][hapmap]
rs6794944	1.00[CEU][hapmap]
rs7644889	1.00[CEU][hapmap]
rs774859	1.00[CEU][hapmap]

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	nsv829676	chr3:111464087-111619200	Genic enhancers Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1295993	TRAP1	trans	lymphoblastoid	RTeQTL
rs1295993	POP1	trans	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111581400-111593800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr3:111582200-111593200	Weak transcription	Lung	lung
3	chr3:111583800-111591200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:111584400-111591000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:111584600-111590800	Weak transcription	Fetal Kidney	kidney
6	chr3:111584600-111591000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:111584600-111593200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:111584600-111603400	Weak transcription	Fetal Intestine Large	intestine
9	chr3:111584800-111591200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:111585200-111591200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:111585200-111591200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:111585200-111591200	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:111585200-111591200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr3:111585200-111622000	Weak transcription	HSMMtube	muscle
15	chr3:111585400-111591000	Weak transcription	Ovary	ovary
16	chr3:111585400-111592800	Weak transcription	HSMM	muscle
17	chr3:111585400-111593400	Weak transcription	Psoas Muscle	Psoas
18	chr3:111585400-111603400	Weak transcription	Spleen	Spleen
19	chr3:111585400-111609000	Weak transcription	Esophagus	oesophagus
20	chr3:111585600-111591000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:111585600-111592400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:111586400-111593000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:111587000-111590200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:111587000-111591200	Weak transcription	Right Atrium	heart
25	chr3:111587000-111591400	Enhancers	Fetal Heart	heart
26	chr3:111587000-111591600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:111587200-111590400	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr3:111587200-111590800	Weak transcription	Right Ventricle	heart
29	chr3:111587200-111591000	Weak transcription	Aorta	Aorta
30	chr3:111587200-111593000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:111587200-111593200	Weak transcription	Gastric	stomach
32	chr3:111587200-111597200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:111587200-111603000	Weak transcription	Placenta	Placenta
34	chr3:111587600-111590200	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:111587800-111591200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr3:111587800-111599200	Weak transcription	Liver	Liver
37	chr3:111588000-111593800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:111588600-111590200	Enhancers	Fetal Lung	lung
39	chr3:111588600-111591000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:111588800-111592400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:111589000-111590800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr3:111589000-111591000	Weak transcription	Adipose Nuclei	Adipose
43	chr3:111589000-111593200	Enhancers	A549	lung
44	chr3:111589200-111590800	Weak transcription	Colon Smooth Muscle	Colon
45	chr3:111589200-111591200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:111589200-111591400	Strong transcription	HMEC	breast
47	chr3:111589200-111598400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:111589200-111603400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:111589400-111590800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:111589400-111590800	Weak transcription	HepG2	liver

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