Variant report

Variant	rs6759454
Chromosome Location	chr2:53717944-53717945
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	POLR2A	chr2:53717827-53718137	U87	brain:	n/a	n/a
2	EP300	chr2:53717913-53718216	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr2:53717860-53717949	A549	lung:	n/a	n/a
4	CEBPB	chr2:53717882-53718254	IMR90	lung:	n/a	n/a
5	CEBPB	chr2:53717911-53718214	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:53717878-53718085	Gliobla	brain:	n/a	n/a
7	FOS	chr2:53717875-53718075	MCF10A-Er-Src	breast:	n/a	chr2:53717929-53717937
8	RFX5	chr2:53717289-53718354	IMR90	lung:	n/a	n/a

Variant related genes	Relation type
ENSG00000223897	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs17044784	1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs17044786	0.90[EUR][1000 genomes]
rs56720868	0.90[EUR][1000 genomes]
rs57814783	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545349	0.90[EUR][1000 genomes]
rs6545350	0.90[EUR][1000 genomes]
rs6704836	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6705194	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707087	1.00[ASN][1000 genomes]
rs6713068	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720273	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6722171	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727792	0.93[EUR][1000 genomes]
rs6741631	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6745622	1.00[ASN][1000 genomes]
rs6751127	1.00[CHB][hapmap]
rs6756089	0.90[EUR][1000 genomes]
rs6759361	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72908978	1.00[ASN][1000 genomes]
rs72908990	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72908995	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73937308	0.90[EUR][1000 genomes]
rs7595651	0.90[EUR][1000 genomes]
rs9784047	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784059	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs985549	0.90[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	nsv1002145	chr2:53387912-53832213	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv535718	chr2:53387912-53832213	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv997401	chr2:53515629-53863347	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv999571	chr2:53690538-53775723	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1012754	chr2:53690538-53785037	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv457873	chr2:53701324-53785037	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv582009	chr2:53701324-53785037	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53717000-53718200	Enhancers	Brain Anterior Caudate	brain
2	chr2:53717000-53718200	Enhancers	Brain Cingulate Gyrus	brain
3	chr2:53717400-53718000	Enhancers	Brain Hippocampus Middle	brain
4	chr2:53717400-53718200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr2:53717400-53718600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr2:53717400-53718600	Enhancers	HSMM	muscle
7	chr2:53717400-53718800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr2:53717400-53719000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:53717400-53719200	Enhancers	Brain Germinal Matrix	brain
10	chr2:53717400-53719400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:53717600-53718000	Enhancers	Aorta	Aorta
12	chr2:53717600-53718000	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr2:53717600-53718200	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr2:53717600-53718200	Enhancers	Fetal Brain Male	brain
15	chr2:53717600-53718800	Enhancers	HSMMtube	muscle
16	chr2:53717800-53718000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:53717800-53718200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:53717800-53718200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:53717800-53718200	Enhancers	A549	lung
20	chr2:53717800-53718200	Flanking Active TSS	Hela-S3	cervix
21	chr2:53717800-53718600	Enhancers	Stomach Smooth Muscle	stomach

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