Variant report

Variant	rs7409060
Chromosome Location	chr19:56879351-56879352
allele	A/C/G/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	SETDB1	chr19:56879261-56879621	U2OS	brain:	n/a	chr19:56879431-56879440
2	E2F6	chr19:56879325-56879937	H1-hESC	embryonic stem cell:	n/a	chr19:56879431-56879440
3	CBX3	chr19:56879131-56879765	K562	blood:	n/a	n/a
4	EGR1	chr19:56879230-56880062	K562	blood:	n/a	chr19:56879874-56879885 chr19:56879872-56879887 chr19:56879431-56879440 chr19:56879873-56879886
5	GTF2F1	chr19:56879256-56879878	K562	blood:	n/a	n/a
6	NRF1	chr19:56879245-56879843	GM12878	blood:	n/a	chr19:56879429-56879440 chr19:56879430-56879444 chr19:56879430-56879441 chr19:56879427-56879441 chr19:56879430-56879439
7	MAX	chr19:56879243-56880204	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr19:56879206-56880394	H1-hESC	embryonic stem cell:	n/a	n/a
9	TEAD4	chr19:56879241-56879745	K562	blood:	n/a	n/a
10	MAX	chr19:56879250-56879985	H1-hESC	embryonic stem cell:	n/a	n/a
11	E2F6	chr19:56879320-56879850	A549	lung:	n/a	chr19:56879431-56879440
12	POLR2A	chr19:56879237-56879945	K562	blood:	n/a	n/a
13	POLR2A	chr19:56879131-56880092	H1-neurons	neurons:	n/a	n/a
14	TAF1	chr19:56879224-56880118	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr19:56879233-56879964	GM12891	blood:	n/a	n/a
16	NRF1	chr19:56878841-56880268	SK-N-SH	brain:	n/a	chr19:56879429-56879440 chr19:56879430-56879444 chr19:56879430-56879441 chr19:56879427-56879441 chr19:56879430-56879439
17	TBP	chr19:56879307-56880000	K562	blood:	n/a	n/a
18	MAX	chr19:56879278-56880040	H1-hESC	embryonic stem cell:	n/a	n/a
19	CREB1	chr19:56879323-56879896	K562	blood:	n/a	n/a
20	POLR2A	chr19:56879160-56879967	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr19:56879217-56880032	K562	blood:	n/a	n/a
22	TEAD4	chr19:56879350-56879887	ECC-1	luminal epithelium:	n/a	n/a
23	TEAD4	chr19:56879339-56879797	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr19:56879270-56879964	HepG2	liver:	n/a	n/a
25	EP300	chr19:56879226-56879790	K562	blood:	n/a	n/a
26	TAL1	chr19:56879340-56879797	K562	blood:	n/a	n/a
27	CREB1	chr19:56879241-56880148	HepG2	liver:	n/a	n/a
28	CREB1	chr19:56879256-56879880	H1-hESC	embryonic stem cell:	n/a	n/a
29	JUND	chr19:56879280-56879881	K562	blood:	n/a	n/a
30	TRIM28	chr19:56879176-56879869	K562	blood:	n/a	n/a
31	TAF7	chr19:56879326-56880040	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:56879294-56879917	NB4	blood:	n/a	n/a
33	BHLHE40	chr19:56879287-56880148	K562	blood:	n/a	n/a
34	NRF1	chr19:56879229-56879849	K562	blood:	n/a	chr19:56879429-56879440 chr19:56879430-56879444 chr19:56879430-56879441 chr19:56879427-56879441 chr19:56879430-56879439
35	TBL1XR1	chr19:56879323-56879513	K562	blood:	n/a	n/a
36	JUND	chr19:56879337-56880170	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr19:56879198-56880000	K562	blood:	n/a	n/a
38	TCF12	chr19:56879308-56880063	A549	lung:	n/a	n/a
39	MYC	chr19:56879219-56880002	K562	blood:	n/a	n/a
40	CREB1	chr19:56879321-56879804	A549	lung:	n/a	n/a
41	MAX	chr19:56879279-56879976	HepG2	liver:	n/a	n/a
42	ZNF143	chr19:56879256-56879973	K562	blood:	n/a	n/a
43	NRF1	chr19:56879256-56879769	HepG2	liver:	n/a	chr19:56879429-56879440 chr19:56879430-56879444 chr19:56879430-56879441 chr19:56879427-56879441 chr19:56879430-56879439
44	E2F6	chr19:56879184-56880102	A549	lung:	n/a	chr19:56879431-56879440
45	POLR2A	chr19:56879187-56879923	HepG2	liver:	n/a	n/a
46	CREB1	chr19:56879280-56879816	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAX	chr19:56879303-56880030	K562	blood:	n/a	n/a
48	POLR2A	chr19:56879180-56880207	H1-hESC	embryonic stem cell:	n/a	n/a
49	HEY1	chr19:56879198-56879967	HepG2	liver:	n/a	n/a
50	MAZ	chr19:56879318-56880003	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56878151..56881655-chr19:56903333..56906269,7	K562	blood:
2	chr19:56874655..56877497-chr19:56878126..56879780,2	K562	blood:
3	chr19:56878056..56881655-chr19:56903333..56906269,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZSCAN5A-3	chr19:56879224-56879422	ENSG00000267606.1

Variant related genes	Relation type
ZNF542	TF binding region
ENSG00000267606	TF binding region
ENSG00000267606	Chromatin interaction
ENSG00000018869	Chromatin interaction
ENSG00000267454	Chromatin interaction

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

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

rs_ID	r²[population]
rs34157829	0.86[ASN][1000 genomes]
rs34175124	0.86[ASN][1000 genomes]
rs34754589	0.86[ASN][1000 genomes]
rs35117763	0.86[ASN][1000 genomes]
rs35570078	0.86[ASN][1000 genomes]
rs36029220	0.86[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	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56872200-56879400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:56878800-56879600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:56878800-56880200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:56878800-56880200	Active TSS	Brain Cingulate Gyrus	brain
5	chr19:56878800-56880400	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr19:56878800-56880600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr19:56878800-56880600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr19:56878800-56880600	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr19:56878800-56880800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr19:56879000-56879400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr19:56879000-56879400	Flanking Active TSS	K562	blood
12	chr19:56879000-56879600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr19:56879000-56879600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr19:56879000-56879600	Active TSS	Fetal Muscle Trunk	muscle
15	chr19:56879000-56879800	Active TSS	Primary hematopoietic stem cells	blood
16	chr19:56879000-56879800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:56879000-56880000	Active TSS	Primary T cells from cord blood	blood
18	chr19:56879000-56880000	Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr19:56879000-56880000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr19:56879000-56880000	Active TSS	Adipose Nuclei	Adipose
21	chr19:56879000-56880000	Active TSS	Brain Angular Gyrus	brain
22	chr19:56879000-56880000	Active TSS	Stomach Smooth Muscle	stomach
23	chr19:56879000-56880000	Active TSS	NH-A	brain
24	chr19:56879000-56880200	Active TSS	Primary T helper naive cells from peripheral blood	blood
25	chr19:56879000-56880200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr19:56879000-56880200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:56879000-56880200	Active TSS	Brain Germinal Matrix	brain
28	chr19:56879000-56880200	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr19:56879000-56880200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr19:56879000-56880200	Active TSS	Brain Substantia Nigra	brain
31	chr19:56879000-56880200	Active TSS	Colon Smooth Muscle	Colon
32	chr19:56879000-56880200	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr19:56879000-56880200	Active TSS	Fetal Brain Male	brain
34	chr19:56879000-56880200	Active TSS	Fetal Brain Female	brain
35	chr19:56879000-56880200	Active TSS	Fetal Lung	lung
36	chr19:56879000-56880200	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr19:56879000-56880200	Active TSS	Rectal Smooth Muscle	rectum
38	chr19:56879000-56880200	Active TSS	Right Atrium	heart
39	chr19:56879000-56880200	Active TSS	HSMM	muscle
40	chr19:56879000-56880200	Active TSS	Osteobl	bone
41	chr19:56879000-56880400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:56879000-56880400	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr19:56879000-56880400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr19:56879000-56880400	Active TSS	Muscle Satellite Cultured Cells	--
45	chr19:56879000-56880400	Active TSS	Fetal Kidney	kidney
46	chr19:56879000-56880400	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr19:56879000-56880400	Active TSS	NHEK	skin
48	chr19:56879000-56880600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
49	chr19:56879000-56880600	Active TSS	HUES48 Cell Line	embryonic stem cell
50	chr19:56879000-56880600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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