Variant report

Variant	rs59852988
Chromosome Location	chr20:23406137-23406138
allele	A/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	chr20:23406057-23406338	HepG2	liver:	n/a	chr20:23406242-23406253 chr20:23406243-23406252 chr20:23406241-23406252
2	SETDB1	chr20:23405968-23406910	U2OS	brain:	n/a	n/a
3	CEBPB	chr20:23406102-23406401	K562	blood:	n/a	chr20:23406242-23406253 chr20:23406243-23406252 chr20:23406241-23406252

No.	Distal block	Cell Line	Cell type
1	chr20:23402152..23403758-chr20:23404630..23407146,2	K562	blood:
2	chr20:23400058..23403758-chr20:23404517..23407833,5	K562	blood:
3	chr20:23400281..23403754-chr20:23404807..23406566,3	MCF-7	breast:

Variant related genes	Relation type
NAPB	TF binding region
ENSG00000125814	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10485644	0.96[EUR][1000 genomes]
rs1076777	0.91[EUR][1000 genomes]
rs1122407	0.96[EUR][1000 genomes]
rs12624341	0.93[EUR][1000 genomes]
rs12625187	0.80[EUR][1000 genomes]
rs12625257	0.96[EUR][1000 genomes]
rs12625297	0.96[EUR][1000 genomes]
rs12625468	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12625489	0.96[EUR][1000 genomes]
rs12625959	0.91[EUR][1000 genomes]
rs12625994	0.96[EUR][1000 genomes]
rs16985303	0.96[EUR][1000 genomes]
rs16985337	0.96[EUR][1000 genomes]
rs2273237	0.91[EUR][1000 genomes]
rs34036626	0.96[EUR][1000 genomes]
rs3736756	0.96[EUR][1000 genomes]
rs3761276	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs56393556	0.96[EUR][1000 genomes]
rs56693860	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56725318	0.96[EUR][1000 genomes]
rs57322153	0.96[EUR][1000 genomes]
rs57896475	0.93[EUR][1000 genomes]
rs58338739	0.81[AFR][1000 genomes]
rs60799291	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61024391	0.96[EUR][1000 genomes]
rs61297472	0.96[EUR][1000 genomes]
rs61344818	0.96[EUR][1000 genomes]
rs73901826	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73901859	0.96[EUR][1000 genomes]
rs73901870	0.96[EUR][1000 genomes]
rs8115832	0.96[EUR][1000 genomes]
rs8117246	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8123389	0.96[EUR][1000 genomes]
rs8125332	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063655	chr20:23396649-23489730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv523998	chr20:23405281-23406519	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs59852988	CSTL1	cis	Skin Sun Exposed Lower leg	GTEx
rs59852988	CSTL1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23403200-23406200	Enhancers	Fetal Thymus	thymus
2	chr20:23405600-23406200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
3	chr20:23405600-23406200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr20:23405600-23406200	Flanking Active TSS	HepG2	liver
5	chr20:23405800-23406200	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr20:23405800-23406200	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr20:23406000-23406200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr20:23406000-23406200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr20:23406000-23406600	Enhancers	NHEK	skin

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