Variant report

Variant	rs9563899
Chromosome Location	chr13:61776532-61776533
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	TEAD4	chr13:61776171-61776557	H1-hESC	embryonic stem cell:	n/a	n/a
2	SIN3AK20	chr13:61776216-61776537	H1-hESC	embryonic stem cell:	n/a	n/a
3	TEAD4	chr13:61776180-61776571	H1-hESC	embryonic stem cell:	n/a	n/a
4	EGR1	chr13:61776175-61776541	H1-hESC	embryonic stem cell:	n/a	n/a
5	SP1	chr13:61776138-61776574	H1-hESC	embryonic stem cell:	n/a	chr13:61776526-61776535
6	JUND	chr13:61776167-61776599	H1-hESC	embryonic stem cell:	n/a	n/a
7	SIN3A	chr13:61776158-61776564	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr13:61776158-61776624	H1-hESC	embryonic stem cell:	n/a	n/a
9	YY1	chr13:61776249-61776570	H1-hESC	embryonic stem cell:	n/a	n/a
10	ATF2	chr13:61776209-61776573	H1-hESC	embryonic stem cell:	n/a	n/a
11	TCF12	chr13:61776135-61776670	H1-hESC	embryonic stem cell:	n/a	n/a
12	EP300	chr13:61776221-61776564	H1-hESC	embryonic stem cell:	n/a	n/a
13	TCF12	chr13:61776150-61776574	H1-hESC	embryonic stem cell:	n/a	n/a
14	ZNF274	chr13:61776200-61776552	H1-hESC	embryonic stem cell:	n/a	n/a
15	HDAC2	chr13:61776224-61776560	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
MIR3169	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12584779	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1483698	0.86[EUR][1000 genomes]
rs17059391	0.84[AFR][1000 genomes]
rs7323627	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7333785	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7337453	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73550768	1.00[ASN][1000 genomes]
rs9563883	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9563884	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9563888	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9563894	0.81[AMR][1000 genomes]
rs9563895	1.00[ASN][1000 genomes]
rs9563898	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9570475	0.81[AFR][1000 genomes]
rs9570477	0.84[AFR][1000 genomes]
rs9570479	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9570488	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9570489	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9570490	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9570491	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9570492	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9570494	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9570497	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9570499	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9570500	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9570501	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9570502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9570505	0.80[ASN][1000 genomes]
rs9570511	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9570516	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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	nsv832627	chr13:61642811-61829217	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
2	esv3444432	chr13:61665252-61781081	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
3	nsv900243	chr13:61711163-61799269	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases
4	nsv900244	chr13:61769349-61856666	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:61776000-61776800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:61776200-61776600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
3	chr13:61776200-61777000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr13:61776400-61776600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
5	chr13:61776400-61777000	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell

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