Variant report

Variant	rs3751599
Chromosome Location	chr15:51573533-51573534
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	RAD21	chr15:51573529-51573954	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr15:51573434-51574046	HCT-116	colon:	n/a	chr15:51573740-51573758
3	RAD21	chr15:51572876-51574125	SK-N-SH	brain:	n/a	chr15:51573358-51573370
4	RAD21	chr15:51573467-51574060	A549	lung:	n/a	n/a
5	SMC3	chr15:51573485-51574082	SK-N-SH	brain:	n/a	n/a
6	CTCF	chr15:51573423-51574084	MCF-7	breast:	n/a	chr15:51573740-51573758
7	CTCF	chr15:51573505-51573859	T-47D	breast:	n/a	chr15:51573740-51573758
8	RAD21	chr15:51573488-51573921	ECC-1	luminal epithelium:	n/a	n/a
9	RAD21	chr15:51573458-51573989	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr15:51573470-51574093	MCF-7	breast:	n/a	chr15:51573740-51573758
11	GATA2	chr15:51573053-51573728	SH-SY5Y	brain:	n/a	n/a
12	RAD21	chr15:51573435-51574092	HCT-116	colon:	n/a	n/a
13	ZNF263	chr15:51573467-51573921	HEK293-T-REx	kidney:	n/a	n/a
14	RAD21	chr15:51573442-51574105	MCF-7	breast:	n/a	n/a
15	CTCF	chr15:51573526-51573970	IMR90	lung:	n/a	chr15:51573740-51573758
16	CTCF	chr15:51573500-51573926	A549	lung:	n/a	chr15:51573740-51573758
17	RAD21	chr15:51573455-51574028	HepG2	liver:	n/a	n/a
18	CTCF	chr15:51573421-51574037	SK-N-SH	brain:	n/a	chr15:51573740-51573758
19	CTCF	chr15:51573400-51573550	HEEpiC	esophagus:	n/a	n/a
20	RAD21	chr15:51573446-51574142	MCF-7	breast:	n/a	n/a
21	CTCF	chr15:51573505-51573947	HepG2	liver:	n/a	chr15:51573740-51573758
22	CTCF	chr15:51573458-51574213	A549	lung:	n/a	chr15:51573740-51573758
23	CTCF	chr15:51573526-51573880	H1-hESC	embryonic stem cell:	n/a	chr15:51573740-51573758
24	RAD21	chr15:51573529-51573951	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:51573150..51574316-chr15:51672564..51674447,46	MCF-7	breast:
2	chr15:51573305..51574188-chr15:51674448..51675433,3	MCF-7	breast:
3	chr15:51568163..51571047-chr15:51573352..51576170,3	MCF-7	breast:
4	chr15:51573458..51575048-chr15:51673491..51675129,2	MCF-7	breast:
5	chr15:51573221..51573792-chr15:51694141..51695046,3	MCF-7	breast:
6	chr15:51521363..51522643-chr15:51572808..51574304,5	MCF-7	breast:
7	chr15:51573015..51575119-chr15:51672522..51674124,19	MCF-7	breast:
8	chr15:51522665..51523209-chr15:51573301..51573878,2	MCF-7	breast:
9	chr15:51572199..51575130-chr15:51658067..51661201,3	MCF-7	breast:
10	chr15:51454742..51455524-chr15:51573036..51574231,4	MCF-7	breast:
11	chr15:51573305..51574299-chr15:51673096..51674022,6	K562	blood:
12	chr15:51573082..51574263-chr15:51693734..51694751,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259701	TF binding region
CYP19A1	TF binding region
ENSG00000259194	Chromatin interaction
ENSG00000137869	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17704533	1.00[AMR][1000 genomes]
rs34600565	1.00[AMR][1000 genomes]
rs56858680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
3	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv904215	chr15:51542193-51673125	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	23456168	GWAS catalog

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51524800-51574000	Weak transcription	HepG2	liver
2	chr15:51560600-51573600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:51572600-51575200	Genic enhancers	Placenta	Placenta
4	chr15:51573000-51574800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr15:51573200-51575000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:51573400-51573600	Enhancers	Brain Substantia Nigra	brain
7	chr15:51573400-51573800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:51573400-51574600	Enhancers	Fetal Stomach	stomach
9	chr15:51573400-51574800	Enhancers	Adipose Nuclei	Adipose
10	chr15:51573400-51575000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr15:51573400-51575000	Enhancers	Fetal Muscle Leg	muscle
12	chr15:51573400-51575200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:51573400-51575400	Enhancers	Brain Hippocampus Middle	brain

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