Variant report

Variant	rs62115496
Chromosome Location	chr19:53636348-53636349
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	NRF1	chr19:53635774-53636592	SK-N-SH	brain:	n/a	chr19:53636160-53636174 chr19:53636163-53636172 chr19:53636165-53636174 chr19:53636163-53636174 chr19:53636212-53636221 chr19:53636163-53636177
2	E2F6	chr19:53635300-53636432	H1-hESC	embryonic stem cell:	n/a	chr19:53636164-53636173 chr19:53635683-53635698
3	MAX	chr19:53635805-53636397	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr19:53635796-53636391	SK-N-MC	brain:	n/a	n/a
5	MXI1	chr19:53635329-53637092	SK-N-SH	brain:	n/a	n/a
6	MAX	chr19:53635486-53636365	SK-N-SH	brain:	n/a	n/a
7	NRF1	chr19:53635990-53636600	H1-hESC	embryonic stem cell:	n/a	chr19:53636160-53636174 chr19:53636163-53636172 chr19:53636165-53636174 chr19:53636163-53636174 chr19:53636212-53636221 chr19:53636163-53636177
8	MXI1	chr19:53635350-53636442	IMR90	lung:	n/a	n/a
9	REST	chr19:53635345-53636503	H1-neurons	neurons:	n/a	chr19:53635755-53635768 chr19:53636040-53636049 chr19:53635730-53635743 chr19:53635818-53635831
10	POLR2A	chr19:53635667-53636382	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr19:53635837-53636399	SK-N-SH	brain:	n/a	n/a
12	MAX	chr19:53635824-53636382	ECC-1	luminal epithelium:	n/a	n/a
13	POLR2A	chr19:53635634-53636385	Gliobla	brain:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:53636347-53636397	GM12892	blood:	n/a
2	chr19:53636309-53636359	U87	brain:	n/a
3	chr19:53636347-53636397	PrEC	prostate:	n/a
4	chr19:53636347-53636397	ovcar-3	ovarian:	n/a
5	chr19:53636309-53636359	Hepatocyte	liver:	n/a
6	chr19:53636309-53636359	Jurkat	blood:	n/a
7	chr19:53636347-53636397	HMEC	breast:	n/a
8	chr19:53636347-53636397	HUVEC	blood vessel:	n/a
9	chr19:53636309-53636359	AG09309	skin:	n/a
10	chr19:53636347-53636397	Hela-S3	cervix:	n/a
11	chr19:53636309-53636359	HIPEpiC	eye:	n/a
12	chr19:53636309-53636359	MCF-7	breast:	n/a
13	chr19:53636347-53636397	HIPEpiC	eye:	n/a
14	chr19:53636347-53636397	HPAEpiC	pulmonary alveolar:	n/a
15	chr19:53636347-53636397	K562	blood:	n/a
16	chr19:53636309-53636359	SKMC	muscle:	n/a
17	chr19:53636347-53636397	MCF10A-Er-Src	breast:	n/a
18	chr19:53636309-53636359	HRCEpiC	kidney:	n/a
19	chr19:53636347-53636397	PANC-1	pancreas:	n/a
20	chr19:53636309-53636359	PFSK-1	brain:	n/a
21	chr19:53636309-53636359	HCM	heart:	n/a
22	chr19:53636347-53636397	HNPCEpiC	eye:	n/a
23	chr19:53636347-53636397	ProgFib	skin:	n/a
24	chr19:53636347-53636397	NHDF-neo	bronchial:	n/a
25	chr19:53636347-53636397	AG04450	lung:	fetal
26	chr19:53636309-53636359	HMEC	breast:	n/a
27	chr19:53636347-53636397	T-47D	breast:	n/a
28	chr19:53636347-53636397	HCPEpiC	choroid plexus:	n/a
29	chr19:53636347-53636397	HRCEpiC	kidney:	n/a
30	chr19:53636309-53636359	AG10803	skin:	n/a
31	chr19:53636347-53636397	GM19239	blood:	n/a
32	chr19:53636347-53636397	HCF	heart:	n/a
33	chr19:53636347-53636397	ECC-1	luminal epithelium:	n/a
34	chr19:53636309-53636359	BE2_C	brain:	n/a
35	chr19:53636347-53636397	HepG2	liver:	n/a
36	chr19:53636309-53636359	HepG2	liver:	n/a
37	chr19:53636309-53636359	SAEC	small airway:	n/a
38	chr19:53636309-53636359	HNPCEpiC	eye:	n/a
39	chr19:53636309-53636359	GM12891	blood:	n/a
40	chr19:53636347-53636397	LNCaP	prostate:	n/a
41	chr19:53636309-53636359	MCF10A-Er-Src	breast:	n/a
42	chr19:53636309-53636359	HCT-116	colon:	n/a
43	chr19:53636309-53636359	HRPEpiC	eye:	n/a
44	chr19:53636347-53636397	Jurkat	blood:	n/a
45	chr19:53636309-53636359	SK-N-MC	brain:	n/a
46	chr19:53636347-53636397	HCM	heart:	n/a
47	chr19:53636309-53636359	BJ	skin:	n/a
48	chr19:53636309-53636359	HAEpiC	amniotic membrane:	n/a
49	chr19:53636309-53636359	NB4	blood:	n/a
50	chr19:53636309-53636359	NHDF-neo	bronchial:	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53605668..53607608-chr19:53634404..53636647,2	MCF-7	breast:

Variant related genes	Relation type
ZNF415	TF binding region
ZNF415	CpG island
ENSG00000170949	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10405714	0.81[EUR][1000 genomes]
rs10405861	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10408257	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10425073	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12973291	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12974598	0.82[EUR][1000 genomes]
rs12975093	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2870444	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34695045	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35400407	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35792558	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35916758	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3930063	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62115495	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62115500	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
7	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
8	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
9	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
10	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
11	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
12	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
14	nsv1061016	chr19:53603952-53641569	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
15	nsv912350	chr19:53636016-53687818	Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62115496	ZNF415	cis	Artery Tibial	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53633600-53636600	Active TSS	Fetal Intestine Large	intestine
2	chr19:53634600-53636600	Flanking Active TSS	Adipose Nuclei	Adipose
3	chr19:53634800-53636400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:53634800-53636600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:53634800-53637800	ZNF genes & repeats	Liver	Liver
6	chr19:53635000-53636400	Active TSS	Fetal Intestine Small	intestine
7	chr19:53635000-53636400	ZNF genes & repeats	Lung	lung
8	chr19:53635000-53636600	Active TSS	H9 Cell Line	embryonic stem cell
9	chr19:53635000-53636600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
10	chr19:53635000-53636600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:53635000-53636600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:53635000-53636600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr19:53635200-53636400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:53635200-53636400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:53635200-53636400	Flanking Active TSS	Fetal Thymus	thymus
16	chr19:53635200-53636400	Active TSS	Thymus	Thymus
17	chr19:53635200-53636400	Active TSS	NH-A	brain
18	chr19:53635200-53636400	Active TSS	NHDF-Ad	bronchial
19	chr19:53635200-53636400	Active TSS	NHLF	lung
20	chr19:53635200-53636600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr19:53635200-53636600	Flanking Active TSS	Primary hematopoietic stem cells	blood
22	chr19:53635200-53636600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:53635200-53636600	Active TSS	Psoas Muscle	Psoas
24	chr19:53635400-53636400	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
25	chr19:53635400-53636400	Active TSS	Primary T cells from cord blood	blood
26	chr19:53635400-53636400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
27	chr19:53635400-53636400	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:53635400-53636400	Active TSS	Aorta	Aorta
29	chr19:53635400-53636400	Active TSS	Brain Angular Gyrus	brain
30	chr19:53635400-53636400	Active TSS	Brain Anterior Caudate	brain
31	chr19:53635400-53636400	Active TSS	Brain Hippocampus Middle	brain
32	chr19:53635400-53636400	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr19:53635400-53636400	Active TSS	Brain Substantia Nigra	brain
34	chr19:53635400-53636400	Active TSS	Fetal Heart	heart
35	chr19:53635400-53636400	Active TSS	Fetal Lung	lung
36	chr19:53635400-53636400	Active TSS	Placenta Amnion	Placenta Amnion
37	chr19:53635400-53636400	Active TSS	HUVEC	blood vessel
38	chr19:53635400-53636600	Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr19:53635400-53636600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
40	chr19:53635400-53636600	Active TSS	Colon Smooth Muscle	Colon
41	chr19:53635400-53636600	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr19:53635400-53636600	Active TSS	Right Ventricle	heart
43	chr19:53635400-53636600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
44	chr19:53635400-53636800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:53635600-53636400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr19:53635600-53636400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:53635600-53636400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:53635600-53636400	Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr19:53635600-53636400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:53635600-53636400	Active TSS	Brain Cingulate Gyrus	brain

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