Variant report

Variant	rs9530505
Chromosome Location	chr13:76589442-76589443
allele	C/T
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	MEF2A	chr13:76588622-76589560	SK-N-SH	brain:	n/a	chr13:76588922-76588937 chr13:76588925-76588934 chr13:76588922-76588936 chr13:76588921-76588937 chr13:76588923-76588934 chr13:76588921-76588936 chr13:76588921-76588936 chr13:76588920-76588941 chr13:76588924-76588935 chr13:76588920-76588941
2	TCF12	chr13:76588474-76589595	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr13:76588487-76589488	SK-N-SH	brain:	n/a	n/a
4	PBX3	chr13:76588897-76589475	SK-N-SH	brain:	n/a	chr13:76589170-76589190
5	GATA3	chr13:76588453-76589489	SK-N-SH	brain:	n/a	n/a
6	EP300	chr13:76589031-76589457	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
LINC01034	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11618070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7335951	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7993854	0.91[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs9573719	0.87[ASN][1000 genomes]
rs9573726	0.90[EUR][1000 genomes]
rs9593151	0.81[EUR][1000 genomes]
rs9600629	0.88[ASN][1000 genomes]
rs972435	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972436	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972437	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997416	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832649	chr13:76424872-76657891	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1054431	chr13:76460431-76885094	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv541837	chr13:76460431-76885094	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv3513085	chr13:76589292-76592118	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3513096	chr13:76589330-76592073	Enhancers Flanking Active TSS Active TSS Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3513107	chr13:76589330-76592073	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76584600-76593800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:76586000-76590200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr13:76587400-76589800	Enhancers	Placenta Amnion	Placenta Amnion
4	chr13:76587600-76590200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr13:76588400-76589600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr13:76588400-76589600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:76588400-76589600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr13:76588400-76589600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:76588400-76589800	Enhancers	Brain Cingulate Gyrus	brain
10	chr13:76588400-76589800	Enhancers	HMEC	breast
11	chr13:76588400-76590000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr13:76588600-76589800	Enhancers	Brain Hippocampus Middle	brain
13	chr13:76589200-76589800	Enhancers	Fetal Lung	lung
14	chr13:76589400-76589800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr13:76589400-76589800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr13:76589400-76589800	Enhancers	Brain Substantia Nigra	brain
17	chr13:76589400-76589800	Flanking Active TSS	Fetal Heart	heart
18	chr13:76589400-76589800	Enhancers	NH-A	brain
19	chr13:76589400-76593200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr13:76589400-76593400	Weak transcription	Brain Angular Gyrus	brain
21	chr13:76589400-76593600	Weak transcription	Aorta	Aorta
22	chr13:76589400-76593800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr13:76589400-76601400	Weak transcription	K562	blood

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