Variant report

Variant	rs552485461
Chromosome Location	chr19:40790770-40790771
allele	A/C
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	POLR2A	chr19:40789333-40791875	GM12878	blood:	n/a	n/a
2	GABPA	chr19:40790770-40791577	HepG2	liver:	n/a	chr19:40791515-40791526 chr19:40790811-40790820 chr19:40791428-40791439 chr19:40791071-40791085 chr19:40791425-40791439 chr19:40791515-40791529 chr19:40791428-40791442 chr19:40791512-40791526 chr19:40791430-40791439
3	POLR2A	chr19:40790287-40791908	K562	blood:	n/a	n/a
4	TBL1XR1	chr19:40790675-40791908	K562	blood:	n/a	n/a
5	EGR1	chr19:40790445-40791565	K562	blood:	n/a	chr19:40790927-40790936 chr19:40791429-40791438 chr19:40791049-40791059 chr19:40790810-40790820 chr19:40791339-40791348 chr19:40790805-40790818 chr19:40790926-40790939 chr19:40790925-40790939 chr19:40790940-40790950 chr19:40790927-40790937 chr19:40791121-40791135 chr19:40790818-40790827 chr19:40790926-40790939 chr19:40790862-40790872 chr19:40791516-40791525 chr19:40790926-40790939 chr19:40790926-40790939 chr19:40791048-40791063 chr19:40790764-40790773
6	TBL1XR1	chr19:40790216-40791906	GM12878	blood:	n/a	n/a
7	GATA3	chr19:40789997-40792033	A549	lung:	n/a	chr19:40791339-40791349
8	MAX	chr19:40790296-40791932	HepG2	liver:	n/a	chr19:40791049-40791059
9	POLR2A	chr19:40789941-40791876	K562	blood:	n/a	n/a
10	POLR2A	chr19:40790235-40791927	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:40788195-40792187	SK-N-MC	brain:	n/a	n/a
12	BACH1	chr19:40790565-40791170	H1-hESC	embryonic stem cell:	n/a	n/a
13	GABPA	chr19:40790539-40791721	K562	blood:	n/a	chr19:40791515-40791526 chr19:40790811-40790820 chr19:40791428-40791439 chr19:40791071-40791085 chr19:40791425-40791439 chr19:40791515-40791529 chr19:40791428-40791442 chr19:40791512-40791526 chr19:40791430-40791439
14	POLR2A	chr19:40790163-40791870	GM15510	blood:	n/a	n/a
15	POU2F2	chr19:40790295-40790771	GM12878	blood:	n/a	n/a
16	TAF1	chr19:40790577-40790885	H1-hESC	embryonic stem cell:	n/a	n/a
17	ETS1	chr19:40790490-40791384	K562	blood:	n/a	chr19:40790925-40790936 chr19:40791339-40791348 chr19:40790835-40790848 chr19:40791049-40791060 chr19:40791339-40791353 chr19:40791340-40791351 chr19:40791335-40791351
18	POLR2A	chr19:40790631-40791236	HCT-116	colon:	n/a	n/a
19	MYC	chr19:40790245-40791846	K562	blood:	n/a	chr19:40791049-40791059
20	POLR2A	chr19:40790645-40790892	H1-hESC	embryonic stem cell:	n/a	n/a
21	MYC	chr19:40790638-40791326	MCF-7	breast:	n/a	chr19:40791049-40791059
22	POLR2A	chr19:40789385-40791876	GM12878	blood:	n/a	n/a
23	HDAC2	chr19:40790666-40791228	HepG2	liver:	n/a	chr19:40790800-40790808
24	TAF1	chr19:40790618-40791303	HepG2	liver:	n/a	n/a
25	EP300	chr19:40790379-40791903	A549	lung:	n/a	chr19:40791338-40791347 chr19:40790813-40790829
26	MAX	chr19:40790489-40791816	Hela-S3	cervix:	n/a	chr19:40791049-40791059
27	E2F6	chr19:40790685-40791634	K562	blood:	n/a	chr19:40791516-40791525 chr19:40790705-40790712 chr19:40790740-40790749 chr19:40791321-40791336 chr19:40790805-40790815 chr19:40791429-40791438
28	POLR2A	chr19:40790467-40791954	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr19:40790578-40791794	HepG2	liver:	n/a	n/a
30	HDAC2	chr19:40790711-40791289	K562	blood:	n/a	chr19:40790800-40790808
31	ZBTB7A	chr19:40790716-40791261	K562	blood:	n/a	chr19:40791028-40791036 chr19:40790741-40790750
32	TAF1	chr19:40790309-40791915	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:40790735-40791946	PFSK-1	brain:	n/a	n/a
34	MAZ	chr19:40790136-40791904	K562	blood:	n/a	chr19:40791049-40791059
35	CTCF	chr19:40790660-40790810	HEK293	kidney:	n/a	n/a
36	MYC	chr19:40790609-40791970	NB4	blood:	n/a	chr19:40791049-40791059
37	ZBTB7A	chr19:40790336-40791375	ECC-1	luminal epithelium:	n/a	chr19:40791028-40791036 chr19:40790741-40790750
38	POLR2A	chr19:40790727-40791232	HUVEC	blood vessel:	n/a	n/a
39	MXI1	chr19:40790475-40791843	HepG2	liver:	n/a	n/a
40	POLR2A	chr19:40788136-40791242	GM12878	blood:	n/a	n/a
41	JUND	chr19:40790545-40791858	A549	lung:	n/a	n/a
42	POLR2A	chr19:40790330-40791963	Raji	blood:	n/a	n/a
43	PAX5	chr19:40790693-40791359	GM12892	blood:	n/a	chr19:40791339-40791348
44	PAX5	chr19:40790258-40791243	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:40790246-40790884	Hela-S3	cervix:	n/a	n/a
46	HCFC1	chr19:40790740-40792125	Hela-S3	cervix:	n/a	n/a
47	HMGN3	chr19:40790646-40791565	K562	blood:	n/a	n/a
48	MAX	chr19:40790603-40791825	GM12878	blood:	n/a	chr19:40791049-40791059
49	SIN3AK20	chr19:40790347-40791759	SK-N-SH	brain:	n/a	n/a
50	TAF1	chr19:40790687-40790878	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40695407..40698481-chr19:40788292..40792778,5	K562	blood:
2	chr19:40789879..40793059-chr19:40870323..40872928,3	K562	blood:
3	chr19:40746630..40748490-chr19:40790537..40793116,2	MCF-7	breast:
4	chr19:40790406..40791402-chr22:50968889..50969883,2	Hela-S3	cervix:
5	chr19:40790365..40793125-chr19:40949596..40951580,2	K562	blood:
6	chr19:40789948..40791553-chr19:41119261..41121070,2	K562	blood:
7	chr19:40788680..40791212-chr19:40852795..40854366,2	K562	blood:

Variant related genes	Relation type
AKT2	TF binding region
MIR641	TF binding region
ENSG00000105223	Chromatin interaction
ENSG00000160392	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000105221	Chromatin interaction
ENSG00000177989	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000130758	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1005660	chr19:40784738-40790835	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
7	esv3373348	chr19:40789637-40792485	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
8	esv3366050	chr19:40790162-40792260	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40789200-40790800	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr19:40789400-40790800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr19:40789400-40791800	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr19:40789600-40791600	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr19:40789600-40792000	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr19:40789600-40792200	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr19:40789800-40790800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr19:40789800-40790800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:40789800-40791000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:40789800-40791200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr19:40789800-40791600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:40789800-40791600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:40789800-40791800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:40790000-40790800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
15	chr19:40790000-40790800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr19:40790000-40790800	Bivalent/Poised TSS	HepG2	liver
17	chr19:40790000-40791200	Active TSS	Gastric	stomach
18	chr19:40790000-40791600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:40790000-40791600	Active TSS	Fetal Kidney	kidney
20	chr19:40790000-40791800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr19:40790000-40791800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr19:40790000-40792000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:40790000-40792000	Active TSS	Ovary	ovary
24	chr19:40790000-40792200	Active TSS	H9 Cell Line	embryonic stem cell
25	chr19:40790000-40792400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:40790200-40790800	Active TSS	Fetal Heart	heart
27	chr19:40790200-40790800	Active TSS	Stomach Mucosa	stomach
28	chr19:40790200-40791400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:40790200-40791400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:40790200-40791600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:40790200-40791600	Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr19:40790200-40791600	Active TSS	Lung	lung
33	chr19:40790200-40791600	Active TSS	A549	lung
34	chr19:40790200-40791600	Active TSS	K562	blood
35	chr19:40790200-40791600	Active TSS	NHLF	lung
36	chr19:40790200-40791800	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr19:40790200-40791800	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr19:40790200-40791800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:40790200-40791800	Active TSS	Esophagus	oesophagus
40	chr19:40790200-40791800	Active TSS	GM12878-XiMat	blood
41	chr19:40790200-40792000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr19:40790200-40792000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:40790200-40792000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:40790200-40792000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:40790200-40792000	Active TSS	Aorta	Aorta
46	chr19:40790200-40792000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:40790200-40792000	Active TSS	Left Ventricle	heart
48	chr19:40790200-40792000	Active TSS	Psoas Muscle	Psoas
49	chr19:40790200-40792000	Active TSS	Right Ventricle	heart
50	chr19:40790200-40792200	Active TSS	Thymus	Thymus

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