Variant report

Variant	rs17424897
Chromosome Location	chr3:111583966-111583967
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:111583879..111585669-chr3:111695722..111698206,2	MCF-7	breast:
2	chr3:111579110..111581393-chr3:111581603..111584247,2	MCF-7	breast:
3	chr3:111581231..111584187-chr3:111592422..111594692,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144827	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1443078	0.87[CEU][hapmap]
rs17429033	1.00[CEU][hapmap]
rs17490485	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs17490973	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs73852716	0.81[AMR][1000 genomes]
rs73852719	0.81[AMR][1000 genomes]

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

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111579400-111585000	Weak transcription	Gastric	stomach
2	chr3:111579600-111584800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:111579800-111584400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:111579800-111588400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:111579800-111589000	Weak transcription	Pancreas	Pancrea
6	chr3:111580000-111589200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:111580400-111584200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:111580400-111584600	Enhancers	HepG2	liver
9	chr3:111580600-111584000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:111580600-111584200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr3:111580600-111584200	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
12	chr3:111580600-111584600	Enhancers	Fetal Stomach	stomach
13	chr3:111580600-111585800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:111580800-111584600	Enhancers	NHDF-Ad	bronchial
15	chr3:111580800-111584800	Enhancers	Liver	Liver
16	chr3:111580800-111585200	Enhancers	HMEC	breast
17	chr3:111581000-111584000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:111581200-111584000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:111581400-111584000	Enhancers	Rectal Smooth Muscle	rectum
20	chr3:111581400-111584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:111581400-111586000	Enhancers	Placenta Amnion	Placenta Amnion
22	chr3:111581400-111593800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:111581600-111584600	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr3:111581600-111584600	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr3:111581600-111584600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:111581800-111584600	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr3:111581800-111585600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:111582000-111584600	Enhancers	Stomach Mucosa	stomach
29	chr3:111582200-111584000	Flanking Active TSS	NH-A	brain
30	chr3:111582200-111584200	Enhancers	HSMMtube	muscle
31	chr3:111582200-111585000	Weak transcription	Left Ventricle	heart
32	chr3:111582200-111585000	Weak transcription	Spleen	Spleen
33	chr3:111582200-111585400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:111582200-111585800	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr3:111582200-111586800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:111582200-111586800	Weak transcription	Placenta	Placenta
37	chr3:111582200-111593200	Weak transcription	Lung	lung
38	chr3:111582600-111584000	Flanking Active TSS	Osteobl	bone
39	chr3:111582600-111584200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:111582800-111584600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr3:111582800-111584600	Enhancers	Fetal Intestine Large	intestine
42	chr3:111583000-111584000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:111583000-111584600	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr3:111583000-111584800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:111583000-111587600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:111583200-111584400	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr3:111583200-111584400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr3:111583200-111584600	Flanking Active TSS	HUVEC	blood vessel
49	chr3:111583200-111585200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr3:111583200-111585200	Enhancers	Fetal Muscle Leg	muscle

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