Variant report

Variant	rs9535645
Chromosome Location	chr13:51907218-51907219
allele	A/C
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	EP300	chr13:51907088-51907527	GM12878	blood:	n/a	n/a
2	EP300	chr13:51907091-51907421	GM12878	blood:	n/a	n/a
3	GATA3	chr13:51907188-51907348	SH-SY5Y	brain:	n/a	chr13:51907289-51907305

Variant related genes	Relation type
SERPINE3	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2274061	1.00[CEU][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2274929	1.00[CEU][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3825524	1.00[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4941696	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4942989	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4942990	0.82[EUR][1000 genomes]
rs4942991	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6561634	0.83[EUR][1000 genomes]
rs7321642	0.88[EUR][1000 genomes]
rs7333661	0.94[EUR][1000 genomes]
rs7333988	0.93[ASW][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7989850	0.82[CEU][hapmap]
rs7996243	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7998084	0.82[CEU][hapmap];0.80[CHD][hapmap]
rs9316539	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9316545	0.82[CEU][hapmap]
rs9526752	1.00[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9526754	0.95[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9526757	1.00[JPT][hapmap]
rs9526764	0.81[CEU][hapmap]
rs9526765	0.81[EUR][1000 genomes]
rs9535653	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9535669	0.83[EUR][1000 genomes]
rs9535670	0.82[CEU][hapmap]
rs9535674	0.83[EUR][1000 genomes]
rs9535696	0.81[CEU][hapmap]
rs9535697	0.81[CEU][hapmap]
rs9568600	0.85[CEU][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap]
rs9568603	0.82[CEU][hapmap];0.80[CHD][hapmap];0.80[GIH][hapmap];0.86[JPT][hapmap]
rs9568612	0.82[CEU][hapmap]
rs9591402	0.82[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9535645	INTS6	Cis_1M	lymphoblastoid	RTeQTL
rs9535645	WDFY2	cis	parietal	SCAN
rs9535645	HNRNPA1L2	cis	cerebellum	SCAN
rs9535645	C13orf18	cis	cerebellum	SCAN
rs9535645	CKAP2	cis	parietal	SCAN
rs9535645	SUCLA2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51867600-51910800	Weak transcription	Pancreas	Pancrea
2	chr13:51900200-51914000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr13:51900400-51938200	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr13:51900800-51913400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:51903400-51913600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr13:51904000-51907800	Enhancers	Fetal Thymus	thymus
7	chr13:51904600-51907800	Enhancers	Primary T cells from cord blood	blood
8	chr13:51905000-51913800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr13:51905400-51915200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:51906000-51917200	Weak transcription	HSMM	muscle
11	chr13:51906000-51944400	Weak transcription	Spleen	Spleen
12	chr13:51906200-51907600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr13:51906200-51935400	Weak transcription	HSMMtube	muscle
14	chr13:51906600-51908600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr13:51906800-51917200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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