Variant report

Variant	rs959518
Chromosome Location	chr1:158169866-158169867
allele	A/G
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	chr1:158169723-158169950	H1-hESC	embryonic stem cell:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
2	FOS	chr1:158169664-158169980	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:158169696-158169974	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:158169672-158169984	MCF10A-Er-Src	breast:	n/a	n/a
5	CEBPB	chr1:158169687-158169961	ECC-1	luminal epithelium:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
6	CEBPB	chr1:158169708-158169982	K562	blood:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
7	CEBPB	chr1:158169713-158170064	ECC-1	luminal epithelium:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
8	MYC	chr1:158169670-158169953	NB4	blood:	n/a	n/a
9	CEBPB	chr1:158169635-158170037	A549	lung:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
10	CEBPB	chr1:158169628-158170039	K562	blood:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
11	CEBPB	chr1:158169667-158170032	IMR90	lung:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
12	CEBPB	chr1:158169661-158170021	A549	lung:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
13	CEBPB	chr1:158169682-158170019	HepG2	liver:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
14	FOS	chr1:158169669-158170002	MCF10A-Er-Src	breast:	n/a	n/a
15	CEBPB	chr1:158169662-158170038	K562	blood:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
16	CEBPB	chr1:158169666-158170030	Hela-S3	cervix:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
17	FOS	chr1:158169660-158169979	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr1:158169744-158169944	MCF10A-Er-Src	breast:	n/a	n/a
19	RUNX3	chr1:158169725-158170074	GM12878	blood:	n/a	n/a
20	CEBPB	chr1:158169625-158170135	A549	lung:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
21	STAT3	chr1:158169806-158169935	MCF10A-Er-Src	breast:	n/a	n/a
22	CEBPB	chr1:158169610-158170075	MCF-7	breast:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
23	CEBPB	chr1:158169696-158170016	MCF-7	breast:	n/a	chr1:158169846-158169855 chr1:158169846-158169855 chr1:158169846-158169855
24	FOS	chr1:158169673-158169978	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000229914	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1042388	0.87[AMR][1000 genomes]
rs12738822	0.91[AMR][1000 genomes]
rs12738901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12744258	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12745422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12751724	0.87[AMR][1000 genomes]
rs3181030	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs34015891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34059172	0.80[AMR][1000 genomes]
rs34120202	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34250639	0.87[AMR][1000 genomes]
rs34431925	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34544089	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34673951	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34811385	0.87[AMR][1000 genomes]
rs35136907	0.91[AMR][1000 genomes]
rs35554638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35669445	0.87[AMR][1000 genomes]
rs7527282	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv872480	chr1:158153526-158450238	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	esv13585	chr1:158159222-158214160	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	esv1814455	chr1:158160528-158200312	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv508626	chr1:158161932-158242158	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv527619	chr1:158168563-158170546	Active TSS Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs959518	GGTA1	trans	lymphoblastoid	seeQTL
rs959518	FSTL3	trans	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158164000-158172800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr1:158167200-158170400	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr1:158168000-158172800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr1:158169200-158170600	Transcr. at gene 5' and 3'	Dnd41	blood
5	chr1:158169400-158170200	Weak transcription	Fetal Thymus	thymus
6	chr1:158169600-158170000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr1:158169600-158170400	Active TSS	Primary T cells from cord blood	blood
8	chr1:158169600-158170600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr1:158169800-158170000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:158169800-158170000	Enhancers	Fetal Lung	lung
11	chr1:158169800-158170000	Flanking Active TSS	Thymus	Thymus

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