Variant report

Variant	rs6485609
Chromosome Location	chr11:45310913-45310914
allele	C/G/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	JUND	chr11:45310899-45311271	Hela-S3	cervix:	n/a	chr11:45311085-45311096 chr11:45311116-45311127
2	USF1	chr11:45310806-45311260	A549	lung:	n/a	n/a
3	STAT3	chr11:45310874-45311221	MCF10A-Er-Src	breast:	n/a	n/a
4	FOSL2	chr11:45310765-45311392	A549	lung:	n/a	n/a
5	FOS	chr11:45310881-45311285	MCF10A-Er-Src	breast:	n/a	n/a
6	FOSL2	chr11:45310857-45311311	SK-N-SH	brain:	n/a	n/a
7	KAP1	chr11:45310839-45311297	U2OS	brain:	n/a	n/a
8	SETDB1	chr11:45310815-45311117	U2OS	brain:	n/a	n/a
9	FOS	chr11:45310908-45311295	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:45305084..45308064-chr11:45308692..45311186,2	K562	blood:

Variant related genes	Relation type
SYT13	TF binding region
ENSG00000019505	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1075778	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769133	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769134	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769135	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10769136	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1077490	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1077491	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838437	0.84[ASN][1000 genomes]
rs10838438	0.87[ASN][1000 genomes]
rs11038372	0.88[ASN][1000 genomes]
rs11038382	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11038384	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11604409	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12363398	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12363412	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2289448	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2863178	0.82[ASN][1000 genomes]
rs2863181	0.90[ASN][1000 genomes]
rs2863182	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2902429	0.82[ASN][1000 genomes]
rs2902433	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34191816	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4556529	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4755306	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4992029	0.84[ASN][1000 genomes]
rs6485605	0.84[ASN][1000 genomes]
rs6485607	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6485608	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7114339	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7117240	0.83[ASN][1000 genomes]
rs7123698	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7123765	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7395289	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7395357	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7395419	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7395421	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7396488	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs751196	0.86[ASN][1000 genomes]
rs7943596	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9300051	0.82[ASN][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	nsv530619	chr11:45294176-45553928	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6485609	SYT13	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45308400-45311200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:45308800-45312400	Weak transcription	Fetal Intestine Large	intestine
3	chr11:45310800-45311200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr11:45310800-45311400	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
5	chr11:45310800-45311600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr11:45310800-45311600	Enhancers	HMEC	breast
7	chr11:45310800-45311600	Enhancers	NH-A	brain

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