Variant report

Variant	rs1564784
Chromosome Location	chr15:74545148-74545149
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74542391..74545216-chr15:74545436..74547097,2	MCF-7	breast:
2	chr15:74544782..74547040-chr15:74550761..74553089,2	MCF-7	breast:
3	chr15:74535160..74537354-chr15:74542878..74545726,2	K562	blood:
4	chr15:74543564..74546354-chr15:74548836..74550787,2	K562	blood:
5	chr15:74534379..74536388-chr15:74543611..74545734,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11629834	0.82[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11632233	0.87[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs11633101	0.92[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs11633321	0.86[ASN][1000 genomes]
rs11638601	0.90[ASN][1000 genomes]
rs11639316	0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11858661	0.86[JPT][hapmap]
rs12898529	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12904523	0.83[ASN][1000 genomes]
rs12905224	0.90[CEU][hapmap];0.97[ASN][1000 genomes]
rs12905234	0.89[ASN][1000 genomes]
rs12905362	0.86[ASN][1000 genomes]
rs12913344	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[ASN][1000 genomes]
rs12913651	0.90[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs168432	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs189497	0.82[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs351153	0.90[CEU][hapmap];0.89[CHB][hapmap];0.97[ASN][1000 genomes]
rs351160	0.82[JPT][hapmap];0.87[MEX][hapmap]
rs351174	0.83[ASN][1000 genomes]
rs351180	0.81[ASN][1000 genomes]
rs351181	0.81[ASN][1000 genomes]
rs3848162	0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs901128	0.82[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv904350	chr15:74500105-74548773	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1564784	NEO1	cis	cerebellum	SCAN
rs1564784	SCAMP5	cis	parietal	SCAN
rs1564784	NRG4	cis	parietal	SCAN
rs1564784	SCAMP2	cis	cerebellum	SCAN
rs1564784	MYO9A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74538800-74545200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:74542000-74546000	Enhancers	Fetal Muscle Leg	muscle
3	chr15:74542000-74546200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr15:74542200-74545800	Enhancers	HSMMtube	muscle
5	chr15:74542200-74546800	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr15:74542400-74545400	Enhancers	Fetal Muscle Trunk	muscle
7	chr15:74542400-74546000	Enhancers	Placenta	Placenta
8	chr15:74542400-74546200	Enhancers	Fetal Brain Male	brain
9	chr15:74542600-74545800	Enhancers	HSMM	muscle
10	chr15:74542600-74546000	Enhancers	Brain Hippocampus Middle	brain
11	chr15:74542600-74547600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr15:74542800-74546000	Enhancers	Brain Substantia Nigra	brain
13	chr15:74542800-74546200	Enhancers	Brain Angular Gyrus	brain
14	chr15:74542800-74546200	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr15:74542800-74546200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr15:74542800-74546200	Enhancers	Fetal Stomach	stomach
17	chr15:74543000-74545800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:74543000-74545800	Enhancers	Left Ventricle	heart
19	chr15:74543000-74546200	Enhancers	Hela-S3	cervix
20	chr15:74543200-74545200	Enhancers	Brain Cingulate Gyrus	brain
21	chr15:74543200-74546200	Enhancers	Spleen	Spleen
22	chr15:74543400-74545400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr15:74543600-74545600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr15:74543800-74545600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr15:74543800-74545800	Enhancers	Right Ventricle	heart
26	chr15:74544000-74545400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:74544000-74545600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr15:74544000-74546200	Enhancers	NHDF-Ad	bronchial
29	chr15:74544000-74546200	Enhancers	Osteobl	bone
30	chr15:74544200-74545600	Weak transcription	Fetal Brain Female	brain
31	chr15:74544200-74546000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:74544200-74546000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr15:74544200-74546200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr15:74544400-74545400	Weak transcription	Brain Germinal Matrix	brain
35	chr15:74544400-74545600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:74544600-74545200	Enhancers	Lung	lung
37	chr15:74544600-74545400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:74544600-74545600	Enhancers	Right Atrium	heart
39	chr15:74544600-74545800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:74544600-74546000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:74544600-74546000	Enhancers	NH-A	brain
42	chr15:74544800-74545200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr15:74544800-74545200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr15:74544800-74545600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr15:74544800-74546200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
46	chr15:74545000-74545200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:74545000-74546000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:74545000-74546000	Weak transcription	Brain Anterior Caudate	brain
49	chr15:74545000-74547000	Weak transcription	Ovary	ovary
50	chr15:74545000-74550600	Weak transcription	Fetal Heart	heart

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