Variant report

Variant	rs62392801
Chromosome Location	chr5:178062267-178062268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr5:178062234-178062372	MCF10A-Er-Src	breast:	n/a	n/a
2	SIN3AK20	chr5:178061975-178062873	MCF-7	breast:	n/a	n/a
3	TEAD4	chr5:178062163-178062584	HepG2	liver:	n/a	n/a
4	HDAC2	chr5:178062171-178062669	MCF-7	breast:	n/a	n/a
5	TEAD4	chr5:178062106-178062744	MCF-7	breast:	n/a	n/a
6	NR2F2	chr5:178062152-178062673	MCF-7	breast:	n/a	n/a
7	FOS	chr5:178062233-178062424	MCF10A-Er-Src	breast:	n/a	n/a
8	TEAD4	chr5:178062127-178062624	MCF-7	breast:	n/a	n/a
9	SIN3AK20	chr5:178062079-178062719	MCF-7	breast:	n/a	n/a
10	FOXA2	chr5:178062264-178062484	HepG2	liver:	n/a	n/a
11	GATA3	chr5:178062026-178062795	MCF-7	breast:	n/a	n/a
12	NR2F2	chr5:178062094-178062751	MCF-7	breast:	n/a	n/a
13	GATA3	chr5:178061971-178062821	MCF-7	breast:	n/a	n/a
14	NFIC	chr5:178062165-178062700	ECC-1	luminal epithelium:	n/a	n/a
15	NFIC	chr5:178062066-178062620	ECC-1	luminal epithelium:	n/a	n/a
16	ZNF217	chr5:178062234-178062597	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:178053909..178055898-chr5:178062249..178064358,2	MCF-7	breast:
2	chr5:178056861..178059158-chr5:178059957..178062888,3	MCF-7	breast:
3	chr5:178060070..178062652-chr5:178068693..178071518,2	MCF-7	breast:
4	chr5:178052435..178056379-chr5:178060810..178069102,10	MCF-7	breast:
5	chr5:178051700..178056905-chr5:178058361..178063297,6	K562	blood:
6	chr5:178051406..178054031-chr5:178060222..178062743,2	K562	blood:

No data

Variant related genes	Relation type
CLK4	TF binding region
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10035569	0.92[ASN][1000 genomes]
rs10063148	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10066600	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10070146	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10070856	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10464049	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10464070	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10479431	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10479500	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11747899	0.89[ASN][1000 genomes]
rs12054903	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12188543	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12189095	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12234109	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13181921	0.87[ASN][1000 genomes]
rs2045892	0.90[ASN][1000 genomes]
rs262023	0.80[ASN][1000 genomes]
rs262024	0.82[ASN][1000 genomes]
rs262033	0.83[ASN][1000 genomes]
rs34183525	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34724127	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34893037	0.92[ASN][1000 genomes]
rs35178365	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35604659	0.92[ASN][1000 genomes]
rs35943178	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3925517	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4424014	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4437395	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4579274	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs543862	0.83[ASN][1000 genomes]
rs55724549	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55783860	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57862544	0.90[ASN][1000 genomes]
rs6884172	0.88[ASN][1000 genomes]
rs6884657	0.88[ASN][1000 genomes]
rs71611451	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71611452	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7447517	0.82[ASN][1000 genomes]
rs7700943	0.82[ASN][1000 genomes]
rs7724406	0.82[ASN][1000 genomes]
rs9329047	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62392801	CLK4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178059600-178064000	Weak transcription	Primary B cells from peripheral blood	blood
2	chr5:178061600-178063200	Enhancers	HMEC	breast
3	chr5:178061600-178063400	Enhancers	Placenta	Placenta
4	chr5:178062000-178062400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr5:178062000-178062600	Enhancers	HepG2	liver
6	chr5:178062000-178062800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:178062200-178062800	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr5:178062200-178062800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr5:178062200-178062800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:178062200-178063400	Enhancers	NHEK	skin

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