Variant report

Variant	rs73935215
Chromosome Location	chr19:53580403-53580404
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	ZNF143	chr19:53580090-53580623	H1-hESC	embryonic stem cell:	n/a	n/a
2	GABPA	chr19:53580184-53580537	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr19:53580233-53580470	K562	blood:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
4	CTCF	chr19:53580281-53580433	Hela-S3	cervix:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
5	CTCF	chr19:53580300-53580450	Caco-2	colon:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
6	CTCF	chr19:53580300-53580450	SAEC	small airway:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
7	FOXA1	chr19:53580230-53580412	T-47D	breast:	n/a	n/a
8	TCF12	chr19:53580293-53580532	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr19:53580177-53580535	K562	blood:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
10	CTCF	chr19:53580280-53580430	HEK293	kidney:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
11	RAD21	chr19:53580211-53580472	SK-N-SH_RA	brain:	n/a	chr19:53580351-53580370
12	CTCF	chr19:53580277-53580432	NHEK	skin:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
13	CTCF	chr19:53580302-53580432	GM12891	blood:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
14	RAD21	chr19:53580259-53580431	K562	blood:	n/a	chr19:53580351-53580370
15	CTCF	chr19:53580280-53580430	HRPEpiC	eye:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
16	CTCF	chr19:53580280-53580430	HUVEC	blood vessel:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
17	CTCF	chr19:53580280-53580430	AG04450	lung:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
18	CTCF	chr19:53580277-53580454	ProgFib	skin:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
19	SMC3	chr19:53580273-53580438	K562	blood:	n/a	n/a
20	CTCF	chr19:53580239-53580543	Spleen_OC	spleen:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
21	CTCF	chr19:53580300-53580450	AG10803	skin:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
22	CTCF	chr19:53580260-53580410	GM12872	blood:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
23	CTCF	chr19:53580280-53580430	WERI-Rb-1	eye:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
24	CTCF	chr19:53580300-53580450	NHLF	lung:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
25	CTCF	chr19:53580280-53580430	AG09309	skin:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
26	CTCF	chr19:53580300-53580450	HVMF	connective:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
27	MAX	chr19:53580209-53580708	H1-hESC	embryonic stem cell:	n/a	n/a
28	TEAD4	chr19:53580220-53580709	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr19:53580328-53580434	Hela-S3	cervix:	n/a	chr19:53580351-53580370
30	MAX	chr19:53580256-53580529	H1-hESC	embryonic stem cell:	n/a	n/a
31	RAD21	chr19:53580146-53580611	H1-hESC	embryonic stem cell:	n/a	chr19:53580351-53580370
32	SIN3A	chr19:53580161-53580571	H1-hESC	embryonic stem cell:	n/a	n/a
33	CTCF	chr19:53580187-53580538	H1-hESC	embryonic stem cell:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
34	CTCF	chr19:53580300-53580450	HMEC	breast:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
35	CTCF	chr19:53580300-53580450	HUVEC	blood vessel:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
36	CTCF	chr19:53580226-53580471	HUVEC	blood vessel:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
37	CTCF	chr19:53580280-53580430	HCPEpiC	choroid plexus:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
38	CTCF	chr19:53580300-53580450	AG04450	lung:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
39	CTCF	chr19:53580280-53580430	HCFaa	heart:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
40	MYC	chr19:53580143-53580676	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr19:53580260-53580410	HPF	lung:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
42	CTCF	chr19:53580320-53580470	GM06990	blood:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
43	RAD21	chr19:53580241-53580466	K562	blood:	n/a	chr19:53580351-53580370
44	CTCF	chr19:53580280-53580430	GM12864	blood:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
45	CTCF	chr19:53580320-53580470	NHDF-neo	bronchial:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
46	CTCF	chr19:53580264-53580446	HepG2	liver:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
47	RAD21	chr19:53580228-53580465	HepG2	liver:	n/a	chr19:53580351-53580370
48	CTCF	chr19:53580260-53580410	HCT-116	colon:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368
49	HDAC2	chr19:53580294-53580637	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr19:53580300-53580450	HMF	breast:	n/a	chr19:53580352-53580373 chr19:53580351-53580367 chr19:53580350-53580368

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53580105..53582342-chr19:53607361..53608967,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF415-2	chr19:53580166-53580665	NONHSAT067622

Variant related genes	Relation type
ZNF160	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs55829045	0.89[AFR][1000 genomes]
rs56360960	0.84[AFR][1000 genomes]
rs73935217	0.89[AFR][1000 genomes]
rs73935233	0.89[AFR][1000 genomes]
rs73935235	0.94[AFR][1000 genomes]
rs73935238	0.94[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53564600-53586800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
2	chr19:53564800-53586600	ZNF genes & repeats	Liver	Liver
3	chr19:53568000-53580600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
4	chr19:53568000-53586400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:53568200-53580600	ZNF genes & repeats	Lung	lung
6	chr19:53568400-53580600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr19:53568400-53588600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr19:53570000-53582000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr19:53570200-53580600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
10	chr19:53570200-53580800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
11	chr19:53570200-53587400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:53570600-53589600	ZNF genes & repeats	GM12878-XiMat	blood
13	chr19:53571000-53580600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
14	chr19:53571000-53587200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
15	chr19:53571400-53580600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
16	chr19:53571800-53581200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
17	chr19:53571800-53583400	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
18	chr19:53571800-53586000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
19	chr19:53571800-53586600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
20	chr19:53573400-53580800	Strong transcription	Dnd41	blood
21	chr19:53573600-53580600	Strong transcription	Osteobl	bone
22	chr19:53573600-53581600	ZNF genes & repeats	Fetal Intestine Small	intestine
23	chr19:53573600-53604800	Weak transcription	Hela-S3	cervix
24	chr19:53574200-53584000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:53574600-53582400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:53574800-53580600	Strong transcription	Fetal Thymus	thymus
27	chr19:53574800-53584000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:53574800-53585200	Weak transcription	Psoas Muscle	Psoas
29	chr19:53574800-53599600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:53575000-53580600	ZNF genes & repeats	A549	lung
31	chr19:53575600-53598600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:53575600-53601000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:53576200-53580600	Strong transcription	HSMMtube	muscle
34	chr19:53576200-53586400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
35	chr19:53576400-53580600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
36	chr19:53576400-53580600	ZNF genes & repeats	HSMM	muscle
37	chr19:53576400-53583200	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:53576800-53605200	Weak transcription	Stomach Mucosa	stomach
39	chr19:53577000-53583000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:53577000-53584000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr19:53577200-53580600	Strong transcription	Primary T cells from cord blood	blood
42	chr19:53577400-53587600	Weak transcription	Fetal Brain Male	brain
43	chr19:53577600-53581800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr19:53577600-53587800	Weak transcription	NHLF	lung
45	chr19:53578000-53580600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
46	chr19:53578000-53580600	ZNF genes & repeats	HMEC	breast
47	chr19:53578000-53580800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr19:53578200-53580600	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
49	chr19:53578200-53580600	ZNF genes & repeats	Spleen	Spleen
50	chr19:53578200-53588600	Weak transcription	Fetal Kidney	kidney

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