Variant report

Variant	rs2453580
Chromosome Location	chr17:19438321-19438322
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	chr17:19435840..19438479-chr17:19458086..19460035,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000142494	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11870808	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11871125	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2252281	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2440164	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2440165	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2453578	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2453579	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2453581	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453582	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453583	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2453584	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55661368	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8071709	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs894680	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs894682	0.96[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	nsv428337	chr17:19340045-19585774	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	esv3335342	chr17:19436410-19438558	Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2453580	SLC47A1	cis	Nerve Tibial	GTEx
rs2453580	C17orf76	cis	cerebellum	SCAN
rs2453580	NCOR1	cis	cerebellum	SCAN
rs2453580	NT5M	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19436400-19438400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
2	chr17:19436400-19438400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
3	chr17:19436800-19438400	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:19437400-19438400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:19437400-19438400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
6	chr17:19437400-19438400	Bivalent Enhancer	Fetal Lung	lung
7	chr17:19437600-19438400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
8	chr17:19437600-19438400	Bivalent Enhancer	Fetal Thymus	thymus
9	chr17:19437600-19438800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr17:19437800-19438400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr17:19437800-19438400	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
12	chr17:19437800-19438400	Flanking Bivalent TSS/Enh	Muscle Satellite Cultured Cells	--
13	chr17:19437800-19438400	Bivalent Enhancer	Fetal Intestine Small	intestine
14	chr17:19437800-19438400	Enhancers	Lung	lung
15	chr17:19437800-19438400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
16	chr17:19437800-19438400	Flanking Active TSS	A549	lung
17	chr17:19437800-19438400	Bivalent Enhancer	HMEC	breast
18	chr17:19437800-19438400	Bivalent Enhancer	HSMM	muscle
19	chr17:19437800-19438400	Flanking Bivalent TSS/Enh	NHEK	skin
20	chr17:19437800-19438600	Bivalent Enhancer	Spleen	Spleen
21	chr17:19437800-19441400	Weak transcription	Pancreas	Pancrea
22	chr17:19437800-19441800	Weak transcription	Gastric	stomach
23	chr17:19438000-19438400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr17:19438000-19438400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
25	chr17:19438000-19438400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
26	chr17:19438000-19438400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr17:19438000-19438400	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:19438000-19438400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr17:19438000-19438400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
30	chr17:19438000-19438400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
31	chr17:19438000-19438400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr17:19438000-19438400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
33	chr17:19438000-19438400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
34	chr17:19438000-19438400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
35	chr17:19438000-19438400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr17:19438000-19438400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr17:19438000-19438400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr17:19438000-19438400	Enhancers	Aorta	Aorta
39	chr17:19438000-19438400	Flanking Active TSS	Liver	Liver
40	chr17:19438000-19438400	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr17:19438000-19438400	Enhancers	Brain Substantia Nigra	brain
42	chr17:19438000-19438400	Bivalent Enhancer	Colonic Mucosa	Colon
43	chr17:19438000-19438400	Enhancers	Esophagus	oesophagus
44	chr17:19438000-19438400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr17:19438000-19438400	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr17:19438000-19438400	Bivalent Enhancer	Fetal Stomach	stomach
47	chr17:19438000-19438400	Enhancers	Left Ventricle	heart
48	chr17:19438000-19438400	Enhancers	Ovary	ovary
49	chr17:19438000-19438400	Bivalent Enhancer	Right Ventricle	heart
50	chr17:19438000-19438400	Bivalent Enhancer	HSMMtube	muscle

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