Variant report

Variant	rs1973029
Chromosome Location	chr15:58791332-58791333
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	CHD1	chr15:58790551-58792173	IMR90	lung:	n/a	n/a
2	MYC	chr15:58791088-58791370	MCF10A-Er-Src	breast:	n/a	chr15:58791228-58791239
3	RCOR1	chr15:58790532-58792284	IMR90	lung:	n/a	n/a
4	EP300	chr15:58790809-58791518	ECC-1	luminal epithelium:	n/a	n/a
5	NR3C1	chr15:58790863-58791530	ECC-1	luminal epithelium:	n/a	n/a
6	MAZ	chr15:58790527-58792179	IMR90	lung:	n/a	chr15:58791228-58791239
7	NFIC	chr15:58790913-58791466	ECC-1	luminal epithelium:	n/a	n/a
8	RAD21	chr15:58790828-58791421	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr15:58791200-58791350	AG04449	skin:	n/a	n/a
10	CTCF	chr15:58791220-58791370	HMEC	breast:	n/a	n/a
11	CTCF	chr15:58791256-58791375	NHEK	skin:	n/a	n/a
12	MAX	chr15:58790787-58791595	ECC-1	luminal epithelium:	n/a	chr15:58791228-58791239
13	CTCF	chr15:58791260-58791410	WERI-Rb-1	eye:	n/a	n/a
14	TCF12	chr15:58790730-58791588	ECC-1	luminal epithelium:	n/a	n/a
15	MAFK	chr15:58790912-58791390	IMR90	lung:	n/a	n/a
16	MXI1	chr15:58790662-58792471	IMR90	lung:	n/a	n/a
17	CEBPB	chr15:58790900-58791368	IMR90	lung:	n/a	n/a
18	CTCF	chr15:58791260-58791410	NHEK	skin:	n/a	n/a
19	TCF12	chr15:58790740-58791555	ECC-1	luminal epithelium:	n/a	n/a
20	CTCF	chr15:58791220-58791370	AG09319	gingival:	n/a	n/a
21	CTCF	chr15:58791220-58791370	WERI-Rb-1	eye:	n/a	n/a
22	USF1	chr15:58790996-58791451	ECC-1	luminal epithelium:	n/a	n/a
23	CTCF	chr15:58791200-58791350	HFF	foreskin:	n/a	n/a
24	MAX	chr15:58790767-58791634	ECC-1	luminal epithelium:	n/a	chr15:58791228-58791239
25	CTCF	chr15:58791200-58791350	RPTEC	kidney:	n/a	n/a
26	CTCF	chr15:58791260-58791410	NHDF-neo	bronchial:	n/a	n/a
27	RAD21	chr15:58790849-58791722	IMR90	lung:	n/a	n/a
28	MAX	chr15:58791045-58791361	K562	blood:	n/a	chr15:58791228-58791239
29	SETDB1	chr15:58790968-58791360	U2OS	brain:	n/a	n/a
30	EP300	chr15:58790793-58791647	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr15:58791220-58791370	HCPEpiC	choroid plexus:	n/a	n/a

Variant related genes	Relation type
ENSG00000259293	TF binding region
ALDH1A2	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10152186	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17190594	0.83[AMR][1000 genomes]
rs2414586	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7180625	0.81[AMR][1000 genomes]
rs72743003	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72743004	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv904268	chr15:58763678-58803225	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58783400-58791600	Enhancers	Fetal Thymus	thymus
2	chr15:58784000-58794800	Weak transcription	Stomach Mucosa	stomach
3	chr15:58784000-58797800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:58784400-58795600	Weak transcription	Liver	Liver
5	chr15:58785000-58797200	Weak transcription	Right Ventricle	heart
6	chr15:58787600-58792600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:58789200-58792600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:58789400-58794600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:58789600-58792200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr15:58789600-58795400	Weak transcription	Thymus	Thymus
11	chr15:58789600-58795600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr15:58790200-58792400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:58790200-58792400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:58790200-58792600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:58790400-58791600	Enhancers	Fetal Kidney	kidney
16	chr15:58790400-58792800	Enhancers	NHDF-Ad	bronchial
17	chr15:58790400-58793200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:58790800-58791400	Enhancers	Adipose Nuclei	Adipose
19	chr15:58790800-58791400	Enhancers	Esophagus	oesophagus
20	chr15:58790800-58791400	Enhancers	Fetal Heart	heart
21	chr15:58790800-58791400	Enhancers	Fetal Muscle Leg	muscle
22	chr15:58790800-58791400	Enhancers	K562	blood
23	chr15:58790800-58791400	Enhancers	NH-A	brain
24	chr15:58790800-58791600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:58790800-58791600	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr15:58790800-58791600	Enhancers	Placenta	Placenta
27	chr15:58790800-58791800	Enhancers	HSMMtube	muscle
28	chr15:58790800-58792200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:58790800-58792200	Enhancers	Osteobl	bone
30	chr15:58791000-58791400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:58791000-58791400	Enhancers	Brain Anterior Caudate	brain
32	chr15:58791000-58791400	Enhancers	Brain Cingulate Gyrus	brain
33	chr15:58791000-58791400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
34	chr15:58791000-58791400	Enhancers	Ovary	ovary
35	chr15:58791000-58791600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:58791000-58791600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:58791000-58791600	Enhancers	HMEC	breast
38	chr15:58791000-58791800	Enhancers	Muscle Satellite Cultured Cells	--
39	chr15:58791000-58792000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:58791000-58792000	Enhancers	NHEK	skin
41	chr15:58791000-58792200	Enhancers	HSMM	muscle
42	chr15:58791200-58791400	Enhancers	Left Ventricle	heart
43	chr15:58791200-58791400	Enhancers	Right Atrium	heart
44	chr15:58791200-58791400	Enhancers	Spleen	Spleen
45	chr15:58791200-58791600	Enhancers	Brain Substantia Nigra	brain
46	chr15:58791200-58791600	Enhancers	A549	lung
47	chr15:58791200-58792200	Enhancers	NHLF	lung

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