Variant report

Variant	rs546804343
Chromosome Location	chr19:42902121-42902122
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	REST	chr19:42900270-42902183	A549	lung:	n/a	n/a
2	MAX	chr19:42900462-42902162	A549	lung:	n/a	chr19:42900536-42900545 chr19:42901461-42901471
3	CTCF	chr19:42902000-42902150	HUVEC	blood vessel:	n/a	n/a
4	CTCF	chr19:42902060-42902210	AG04450	lung:	n/a	n/a
5	MAX	chr19:42900513-42902175	K562	blood:	n/a	chr19:42900536-42900545 chr19:42901461-42901471
6	MAX	chr19:42899884-42902339	A549	lung:	n/a	chr19:42900536-42900545 chr19:42901461-42901471 chr19:42899996-42900005
7	CTCF	chr19:42901980-42902130	SAEC	small airway:	n/a	n/a
8	TCF12	chr19:42900196-42902225	A549	lung:	n/a	chr19:42900975-42900984
9	CTCF	chr19:42902020-42902170	BJ	skin:	n/a	n/a
10	SP1	chr19:42900307-42902155	A549	lung:	n/a	chr19:42901460-42901474 chr19:42901203-42901215 chr19:42901147-42901168 chr19:42901203-42901215 chr19:42901463-42901475 chr19:42901463-42901475
11	SP1	chr19:42900357-42902300	HCT-116	colon:	n/a	chr19:42901460-42901474 chr19:42901203-42901215 chr19:42901147-42901168 chr19:42901203-42901215 chr19:42901463-42901475 chr19:42901463-42901475
12	POLR2A	chr19:42902015-42902165	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr19:42902060-42902210	GM12864	blood:	n/a	n/a
14	E2F6	chr19:42900510-42902261	A549	lung:	n/a	chr19:42901128-42901137 chr19:42901126-42901135
15	ELF1	chr19:42900763-42902131	GM12878	blood:	n/a	chr19:42901326-42901338 chr19:42901458-42901470
16	UBTF	chr19:42902038-42902147	K562	blood:	n/a	n/a
17	CTCF	chr19:42902020-42902170	HCT-116	colon:	n/a	n/a
18	CTCF	chr19:42902040-42902190	HBMEC	blood vessel:	n/a	n/a
19	HNF4A	chr19:42902030-42902210	HepG2	liver:	n/a	chr19:42902127-42902142 chr19:42902128-42902136 chr19:42902129-42902141 chr19:42902128-42902141 chr19:42902129-42902141 chr19:42902127-42902142 chr19:42902129-42902141 chr19:42902128-42902142 chr19:42902127-42902142 chr19:42902129-42902141 chr19:42902127-42902142
20	CTCF	chr19:42902060-42902210	HCM	heart:	n/a	n/a
21	CTCF	chr19:42902020-42902170	HAc	cerebellar:	n/a	n/a
22	CTCF	chr19:42901980-42902130	AG04449	skin:	n/a	n/a
23	PBX3	chr19:42900519-42902153	A549	lung:	n/a	chr19:42901238-42901258
24	POLR2A	chr19:42901860-42902199	K562	blood:	n/a	n/a
25	KAP1	chr19:42900577-42902204	HEK293	kidney:	n/a	n/a
26	CTCF	chr19:42901980-42902130	A549	lung:	n/a	n/a
27	BCL3	chr19:42900101-42902425	A549	lung:	n/a	n/a
28	CTCF	chr19:42901980-42902130	SK-N-SH_RA	brain:	n/a	n/a
29	POLR2A	chr19:42901997-42902275	K562	blood:	n/a	n/a
30	CTCF	chr19:42901980-42902130	GM12873	blood:	n/a	n/a
31	POLR2A	chr19:42901830-42902139	GM12878	blood:	n/a	n/a
32	ZNF263	chr19:42900573-42902158	HEK293-T-REx	kidney:	n/a	chr19:42901465-42901474

No.	Distal block	Cell Line	Cell type
1	chr19:42746379..42748753-chr19:42901046..42902799,2	K562	blood:
2	chr19:42900633..42903687-chr19:42904617..42908034,6	MCF-7	breast:
3	chr19:42900819..42903655-chr19:42904775..42907143,2	MCF-7	breast:
4	chr19:42901625..42903508-chr19:42904581..42908984,3	K562	blood:
5	chr19:42895668..42898012-chr19:42901990..42905454,3	K562	blood:
6	chr19:42900679..42903538-chr19:42909669..42912049,2	K562	blood:
7	chr19:42894017..42895736-chr19:42900827..42903287,2	MCF-7	breast:
8	chr19:42805304..42808319-chr19:42899510..42903078,3	K562	blood:
9	chr19:42901013..42903466-chr19:42908156..42911805,3	MCF-7	breast:

Variant related genes	Relation type
LIPE-AS1	TF binding region
ENSG00000079435	Chromatin interaction
ENSG00000105723	Chromatin interaction
ENSG00000105427	Chromatin interaction
ENSG00000188368	Chromatin interaction
ENSG00000079462	Chromatin interaction
ENSG00000213904	Chromatin interaction
ENSG00000204957	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers 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	71 gene(s)	inside rSNPs	diseases
4	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
6	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
7	nsv911788	chr19:42887492-42930652	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv911789	chr19:42901430-42906725	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv911790	chr19:42901430-42908074	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv911791	chr19:42901430-42909478	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv911792	chr19:42901430-42929254	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv911793	chr19:42901430-42929502	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
13	nsv911794	chr19:42901430-42930652	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
14	nsv911795	chr19:42901430-42932699	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42900200-42902200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr19:42900400-42902200	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr19:42900400-42902400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:42900400-42902400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr19:42900400-42902400	Flanking Active TSS	NHEK	skin
6	chr19:42900600-42902200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:42900600-42902200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr19:42900600-42902200	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr19:42900600-42902200	Flanking Active TSS	Fetal Muscle Trunk	muscle
10	chr19:42900600-42902200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr19:42900600-42902200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr19:42900600-42902200	Flanking Active TSS	HSMM	muscle
13	chr19:42900600-42902200	Flanking Active TSS	HUVEC	blood vessel
14	chr19:42900600-42902400	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr19:42900600-42902400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:42900600-42902400	Flanking Active TSS	HMEC	breast
17	chr19:42901000-42902200	Active TSS	HSMMtube	muscle
18	chr19:42901400-42902200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr19:42901400-42902200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr19:42901400-42902200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:42901400-42902200	Flanking Active TSS	Colon Smooth Muscle	Colon
22	chr19:42901400-42902200	Flanking Active TSS	Duodenum Mucosa	Duodenum
23	chr19:42901400-42902200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr19:42901400-42902200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
25	chr19:42901400-42902200	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr19:42901400-42902200	Flanking Active TSS	K562	blood
27	chr19:42901400-42902200	Flanking Active TSS	Osteobl	bone
28	chr19:42901400-42902400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:42901400-42902400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
30	chr19:42901400-42902400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
31	chr19:42901400-42902400	Flanking Active TSS	Dnd41	blood
32	chr19:42901400-42902400	Flanking Active TSS	Hela-S3	cervix
33	chr19:42901600-42902200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
34	chr19:42901600-42902200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr19:42901600-42902200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:42901600-42902200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr19:42901600-42902200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:42901600-42902200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:42901600-42902200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
40	chr19:42901600-42902200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr19:42901600-42902200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
42	chr19:42901600-42902200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
43	chr19:42901600-42902200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr19:42901600-42902200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr19:42901600-42902200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr19:42901600-42902200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr19:42901600-42902200	Flanking Bivalent TSS/Enh	Liver	Liver
48	chr19:42901600-42902200	Flanking Active TSS	Brain Cingulate Gyrus	brain
49	chr19:42901600-42902200	Flanking Active TSS	Brain Germinal Matrix	brain
50	chr19:42901600-42902200	Flanking Active TSS	Brain Substantia Nigra	brain

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