Variant report

Variant	rs1539512
Chromosome Location	chr10:54739291-54739292
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	CEBPB	chr10:54739102-54739456	A549	lung:	n/a	chr10:54739271-54739284 chr10:54739272-54739283
2	FOS	chr10:54739141-54739708	MCF10A-Er-Src	breast:	n/a	n/a
3	CEBPB	chr10:54739108-54739602	Hela-S3	cervix:	n/a	chr10:54739271-54739284 chr10:54739272-54739283
4	CEBPB	chr10:54739135-54739420	H1-hESC	embryonic stem cell:	n/a	chr10:54739271-54739284 chr10:54739272-54739283
5	FOS	chr10:54739171-54739691	MCF10A-Er-Src	breast:	n/a	n/a
6	STAT3	chr10:54739196-54739741	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT3	chr10:54739285-54739702	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr10:54739153-54739734	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr10:54739247-54739737	MCF10A-Er-Src	breast:	n/a	n/a
10	CEBPB	chr10:54739186-54739365	MCF-7	breast:	n/a	chr10:54739271-54739284 chr10:54739272-54739283
11	JUND	chr10:54739186-54739421	HepG2	liver:	n/a	n/a
12	CEBPB	chr10:54739101-54739452	HepG2	liver:	n/a	chr10:54739271-54739284 chr10:54739272-54739283
13	FOS	chr10:54739183-54739744	MCF10A-Er-Src	breast:	n/a	n/a
14	JUN	chr10:54739189-54739384	HepG2	liver:	n/a	chr10:54739269-54739282
15	CEBPB	chr10:54739118-54739626	IMR90	lung:	n/a	chr10:54739271-54739284 chr10:54739272-54739283

Variant related genes	Relation type
ENSG00000227121	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10824848	0.89[EUR][1000 genomes]
rs10824853	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11003294	0.91[EUR][1000 genomes]
rs11003295	0.91[EUR][1000 genomes]
rs11003303	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1343051	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1343052	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1343070	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1880396	0.93[EUR][1000 genomes]
rs1880397	0.88[ASN][1000 genomes]
rs1917162	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1917165	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1917166	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1917171	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1935936	0.90[ASN][1000 genomes]
rs1949816	0.87[ASN][1000 genomes]
rs2066436	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2140671	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2244530	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2244637	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2244778	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2248899	0.88[ASN][1000 genomes]
rs2249349	0.87[ASN][1000 genomes]
rs2249356	0.87[ASN][1000 genomes]
rs2253123	0.88[ASN][1000 genomes]
rs2384100	0.83[ASN][1000 genomes]
rs2462480	0.88[ASN][1000 genomes]
rs2488606	0.86[ASN][1000 genomes]
rs2492355	0.86[ASN][1000 genomes]
rs4935055	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7095436	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7902771	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895404	chr10:54545590-54850707	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv831877	chr10:54565135-54764638	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1043809	chr10:54645158-54860817	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv540627	chr10:54645158-54860817	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv467201	chr10:54697623-54929003	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv550906	chr10:54697623-54929003	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv470939	chr10:54700783-54917339	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv508584	chr10:54704765-54747382	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv467202	chr10:54735164-54830687	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv550907	chr10:54735164-54830687	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1539512	RP11-319F12.2	cis	Thyroid	GTEx
rs1539512	TMOD2	trans	cerebellum	SCAN
rs1539512	ALS2	trans	cerebellum	SCAN
rs1539512	NMT2	trans	lymphoblastoid	seeQTL
rs1539512	PCDH15	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:54734600-54764600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr10:54737600-54743200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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