Variant report

Variant	rs6561691
Chromosome Location	chr13:53477132-53477133
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1323117	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1885848	0.80[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4886022	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4886033	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886034	0.84[ASN][1000 genomes]
rs496890	0.83[ASN][1000 genomes]
rs525135	0.80[ASN][1000 genomes]
rs664608	0.83[ASN][1000 genomes]
rs676284	0.80[ASN][1000 genomes]
rs912091	0.94[ASN][1000 genomes]
rs9316593	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9316594	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9527030	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9536315	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9596709	0.92[ASN][1000 genomes]
rs9596710	0.92[ASN][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	nsv530719	chr13:53173014-53675953	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv3440613	chr13:53307609-53671072	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv900090	chr13:53429453-53495715	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6561691	DLEU7	cis	parietal	SCAN
rs6561691	OLFM4	cis	cerebellum	SCAN
rs6561691	C20orf72	trans	cerebellum	SCAN
rs6561691	RB1	cis	parietal	SCAN
rs6561691	DLEU1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53471400-53478400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:53471600-53478600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr13:53471600-53478600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:53471600-53479200	Weak transcription	Brain Hippocampus Middle	brain
5	chr13:53476000-53482200	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr13:53476200-53477400	Enhancers	H9 Cell Line	embryonic stem cell
7	chr13:53476200-53480200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr13:53476200-53481000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:53476200-53482400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr13:53476400-53482000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr13:53476600-53477400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr13:53476600-53478000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr13:53476600-53478000	Enhancers	GM12878-XiMat	blood
14	chr13:53476600-53480600	Enhancers	Brain Germinal Matrix	brain
15	chr13:53476600-53481200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr13:53476600-53482400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr13:53476800-53478800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr13:53476800-53482000	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr13:53477000-53477200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr13:53477000-53478000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr13:53477000-53479000	Enhancers	Fetal Brain Female	brain
22	chr13:53477000-53479400	Enhancers	Fetal Brain Male	brain
23	chr13:53477000-53481000	Enhancers	Cortex derived primary cultured neurospheres	brain

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