Variant report

Variant	rs9550472
Chromosome Location	chr13:30064363-30064364
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	GATA2	chr13:30064083-30064462	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
MTUS2-AS1	TF binding region

Extended variants
information (count: 5 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs7324267	0.93[ASW][hapmap];1.00[CHD][hapmap];0.92[LWK][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv983696	chr13:30034016-30090454	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv430551	chr13:30061100-30113000	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	esv3354076	chr13:30063952-30068350	Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv899960	chr13:30064014-30097240	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9550472	C13orf26	cis	parietal	SCAN
rs9550472	BRCA2	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30047200-30081000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:30055600-30070200	Weak transcription	Ovary	ovary
3	chr13:30057400-30070200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:30058200-30070200	Weak transcription	Right Ventricle	heart
5	chr13:30058800-30068200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr13:30058800-30070200	Weak transcription	Right Atrium	heart
7	chr13:30059200-30065800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:30059400-30065800	Weak transcription	Dnd41	blood
9	chr13:30062000-30070200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr13:30062200-30066400	Weak transcription	Aorta	Aorta
11	chr13:30062400-30065200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr13:30062400-30066600	Weak transcription	Fetal Muscle Leg	muscle
13	chr13:30062400-30068400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:30062400-30087200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr13:30062600-30065200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr13:30062600-30066800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr13:30063000-30066000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr13:30063600-30064400	Strong transcription	Fetal Heart	heart
19	chr13:30063600-30070600	Weak transcription	Brain Angular Gyrus	brain
20	chr13:30064000-30070200	Weak transcription	Left Ventricle	heart
21	chr13:30064200-30065000	Enhancers	Fetal Brain Female	brain
22	chr13:30064200-30066200	Enhancers	Fetal Brain Male	brain

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