Variant report

Variant	rs13188088
Chromosome Location	chr5:79701839-79701840
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:79701720-79702093	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79694018..79695713-chr5:79701443..79703273,2	MCF-7	breast:

Variant related genes	Relation type
ZFYVE16	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs13187593	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34748622	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62365285	0.90[ASN][1000 genomes]
rs62367060	1.00[ASN][1000 genomes]
rs6453514	1.00[JPT][hapmap]
rs6882754	0.83[EUR][1000 genomes]
rs7712536	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7730069	1.00[LWK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948807	chr5:79549207-79805765	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv518480	chr5:79586085-79748382	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1028027	chr5:79694699-79841752	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13188088	SPZ1	cis	cerebellum	SCAN
rs13188088	ZCCHC9	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79695400-79702400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:79695600-79702400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:79695600-79702600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:79695600-79702600	Weak transcription	Brain Hippocampus Middle	brain
5	chr5:79695600-79702600	Weak transcription	Osteobl	bone
6	chr5:79695800-79702000	Weak transcription	Brain Anterior Caudate	brain
7	chr5:79695800-79702200	Weak transcription	Brain Substantia Nigra	brain
8	chr5:79695800-79702400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr5:79695800-79702600	Weak transcription	Adipose Nuclei	Adipose
10	chr5:79695800-79702600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr5:79695800-79702600	Weak transcription	GM12878-XiMat	blood
12	chr5:79696200-79702600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:79697000-79702200	Weak transcription	Primary neutrophils fromperipheralblood	blood
14	chr5:79697200-79702800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:79698800-79702800	Weak transcription	Pancreas	Pancrea
16	chr5:79700000-79702200	Weak transcription	HepG2	liver
17	chr5:79700400-79702000	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:79700600-79702200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr5:79700800-79702600	Weak transcription	Liver	Liver
20	chr5:79701800-79702000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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