Variant report

Variant	rs73562123
Chromosome Location	chr19:51897486-51897487
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	MTA3	chr19:51897045-51899150	GM12878	blood:	n/a	n/a
2	GABPA	chr19:51897343-51898041	K562	blood:	n/a	chr19:51897759-51897768 chr19:51897837-51897846 chr19:51897837-51897848 chr19:51897834-51897848
3	NFYB	chr19:51897382-51897969	Hela-S3	cervix:	n/a	chr19:51897652-51897667 chr19:51897709-51897723 chr19:51897712-51897724 chr19:51897708-51897723 chr19:51897655-51897665 chr19:51897654-51897669 chr19:51897652-51897667 chr19:51897711-51897721 chr19:51897710-51897723 chr19:51897708-51897723
4	TAF1	chr19:51897208-51898127	A549	lung:	n/a	n/a
5	BHLHE40	chr19:51897307-51898007	K562	blood:	n/a	n/a
6	GABPA	chr19:51897315-51897788	Hela-S3	cervix:	n/a	chr19:51897759-51897768
7	ZBTB7A	chr19:51897356-51898066	K562	blood:	n/a	n/a
8	ELF1	chr19:51897207-51898093	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:51897369-51898062	Gliobla	brain:	n/a	n/a
10	FOXM1	chr19:51897346-51898056	ECC-1	luminal epithelium:	n/a	n/a
11	ARID3A	chr19:51897142-51897847	K562	blood:	n/a	n/a
12	SRF	chr19:51897353-51897583	H1-hESC	embryonic stem cell:	n/a	chr19:51897462-51897480
13	SPI1	chr19:51897439-51897702	K562	blood:	n/a	n/a
14	GTF2B	chr19:51897425-51898026	K562	blood:	n/a	n/a
15	YY1	chr19:51897135-51897558	GM12892	blood:	n/a	n/a
16	TAF1	chr19:51897166-51898200	H1-hESC	embryonic stem cell:	n/a	n/a
17	MYC	chr19:51897212-51898083	K562	blood:	n/a	n/a
18	SP2	chr19:51897403-51897834	K562	blood:	n/a	chr19:51897710-51897720
19	MYBL2	chr19:51897264-51897971	HepG2	liver:	n/a	n/a
20	POLR2A	chr19:51897419-51898121	HUVEC	blood vessel:	n/a	n/a
21	SP1	chr19:51897233-51897935	H1-hESC	embryonic stem cell:	n/a	chr19:51897667-51897679 chr19:51897667-51897679 chr19:51897701-51897722 chr19:51897517-51897531
22	FOXM1	chr19:51897380-51897921	ECC-1	luminal epithelium:	n/a	n/a
23	YY1	chr19:51897253-51897623	SK-N-SH_RA	brain:	n/a	n/a
24	POLR2A	chr19:51897300-51897626	HepG2	liver:	n/a	n/a
25	ELF1	chr19:51897131-51897924	A549	lung:	n/a	n/a
26	RCOR1	chr19:51897276-51897953	HepG2	liver:	n/a	n/a
27	MAX	chr19:51897288-51898070	H1-hESC	embryonic stem cell:	n/a	n/a
28	STAT3	chr19:51897454-51897901	MCF10A-Er-Src	breast:	n/a	n/a
29	CEBPB	chr19:51897307-51897602	K562	blood:	n/a	n/a
30	NFIC	chr19:51897088-51898048	GM12878	blood:	n/a	chr19:51897220-51897236 chr19:51897219-51897236
31	NFYA	chr19:51897358-51898020	K562	blood:	n/a	chr19:51897652-51897667 chr19:51897709-51897723 chr19:51897712-51897724 chr19:51897708-51897723 chr19:51897655-51897665 chr19:51897652-51897667 chr19:51897711-51897721 chr19:51897710-51897723 chr19:51897708-51897723
32	SP1	chr19:51897056-51898295	HCT-116	colon:	n/a	chr19:51897667-51897679 chr19:51897667-51897679 chr19:51897701-51897722 chr19:51897517-51897531
33	USF2	chr19:51897319-51897662	HepG2	liver:	n/a	n/a
34	MAX	chr19:51897476-51897954	HepG2	liver:	n/a	n/a
35	GABPA	chr19:51897368-51897906	GM12878	blood:	n/a	chr19:51897759-51897768 chr19:51897837-51897846 chr19:51897837-51897848 chr19:51897834-51897848
36	MXI1	chr19:51896896-51898500	SK-N-SH	brain:	n/a	n/a
37	ZBTB7A	chr19:51897315-51898256	K562	blood:	n/a	n/a
38	POLR2A	chr19:51897294-51897530	SK-N-SH	brain:	n/a	n/a
39	GABPA	chr19:51897420-51897847	HepG2	liver:	n/a	chr19:51897759-51897768 chr19:51897837-51897846
40	SP2	chr19:51897393-51897865	H1-hESC	embryonic stem cell:	n/a	chr19:51897710-51897720
41	TAF7	chr19:51897118-51897582	H1-hESC	embryonic stem cell:	n/a	n/a
42	TAF1	chr19:51897247-51898050	H1-hESC	embryonic stem cell:	n/a	n/a
43	ZNF143	chr19:51897384-51897987	K562	blood:	n/a	n/a
44	TBP	chr19:51897195-51898039	GM12878	blood:	n/a	n/a
45	SRF	chr19:51897201-51898048	MCF-7	breast:	n/a	chr19:51897462-51897480
46	CTCF	chr19:51897380-51897530	Caco-2	colon:	n/a	n/a
47	TBL1XR1	chr19:51897190-51898004	GM12878	blood:	n/a	n/a
48	CTCF	chr19:51897268-51897561	Spleen_OC	spleen:	n/a	n/a
49	TBL1XR1	chr19:51897358-51898319	K562	blood:	n/a	n/a
50	POLR2A	chr19:51897363-51898260	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51852221..51854655-chr19:51896063..51897608,2	K562	blood:
2	chr19:51869234..51872471-chr19:51897367..51899516,3	MCF-7	breast:
3	chr19:51895053..51897765-chr19:52007493..52009642,2	K562	blood:
4	chr19:51897297..51899400-chr19:52095029..52099296,3	K562	blood:
5	chr19:51840838..51845657-chr19:51892354..51900411,18	K562	blood:
6	chr19:51896400..51903695-chr19:51903717..51912186,11	K562	blood:
7	chr19:51894435..51896093-chr19:51896097..51897636,2	K562	blood:
8	chr19:51847346..51848930-chr19:51897301..51899895,2	K562	blood:
9	chr19:51841257..51845442-chr19:51896216..51899567,12	K562	blood:
10	chr19:51896384..51897937-chr19:51904154..51907057,2	MCF-7	breast:
11	chr19:51897392..51898223-chr9:20684270..20685038,2	Hela-S3	cervix:
12	chr19:51867772..51875803-chr19:51892381..51899756,21	K562	blood:
13	chr19:51864453..51872845-chr19:51892428..51902096,29	K562	blood:
14	chr19:51889349..51894566-chr19:51895156..51899826,6	K562	blood:
15	chr19:51868903..51871265-chr19:51897328..51899243,2	MCF-7	breast:
16	chr19:51889722..51893942-chr19:51894149..51900029,8	K562	blood:

Variant related genes	Relation type
C19orf84	TF binding region
ENSG00000268889	TF binding region
ENSG00000167765	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000105370	Chromatin interaction
ENSG00000227071	Chromatin interaction
ENSG00000269403	Chromatin interaction
ENSG00000186806	Chromatin interaction
ENSG00000268144	Chromatin interaction
ENSG00000267905	Chromatin interaction
ENSG00000262874	Chromatin interaction
ENSG00000105379	Chromatin interaction
ENSG00000267984	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000268839	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000105374	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs12327847	0.87[AMR][1000 genomes]
rs12327891	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS 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

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51896800-51898000	Enhancers	Sigmoid Colon	Sigmoid Colon
2	chr19:51896800-51898200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:51896800-51898600	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:51897000-51897600	Active TSS	Brain Cingulate Gyrus	brain
5	chr19:51897000-51897800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:51897000-51897800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:51897000-51897800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:51897000-51897800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr19:51897000-51897800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:51897000-51897800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:51897000-51897800	Active TSS	Brain Angular Gyrus	brain
12	chr19:51897000-51897800	Active TSS	Brain Germinal Matrix	brain
13	chr19:51897000-51897800	Active TSS	Brain Hippocampus Middle	brain
14	chr19:51897000-51897800	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr19:51897000-51897800	Active TSS	Colonic Mucosa	Colon
16	chr19:51897000-51897800	Enhancers	Lung	lung
17	chr19:51897000-51897800	Active TSS	Psoas Muscle	Psoas
18	chr19:51897000-51897800	Active TSS	Rectal Mucosa Donor 31	rectum
19	chr19:51897000-51897800	Active TSS	NHLF	lung
20	chr19:51897000-51898000	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr19:51897000-51898000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr19:51897000-51898000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:51897000-51898000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:51897000-51898000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
25	chr19:51897000-51898200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:51897000-51898200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:51897000-51898200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:51897000-51898200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr19:51897000-51898200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr19:51897000-51898200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:51897000-51898200	Flanking Active TSS	Adipose Nuclei	Adipose
32	chr19:51897000-51898200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:51897000-51898200	Active TSS	Fetal Kidney	kidney
34	chr19:51897000-51898200	Active TSS	Fetal Lung	lung
35	chr19:51897000-51898200	Flanking Active TSS	Placenta	Placenta
36	chr19:51897000-51898200	Active TSS	Rectal Mucosa Donor 29	rectum
37	chr19:51897000-51898200	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr19:51897000-51898400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr19:51897000-51898400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr19:51897000-51898400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
41	chr19:51897000-51898400	Flanking Active TSS	Fetal Muscle Trunk	muscle
42	chr19:51897000-51898400	Active TSS	Rectal Smooth Muscle	rectum
43	chr19:51897000-51898400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr19:51897000-51898600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:51897000-51898600	Active TSS	HSMM	muscle
46	chr19:51897000-51898800	Active TSS	H9 Cell Line	embryonic stem cell
47	chr19:51897000-51898800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:51897000-51898800	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr19:51897000-51898800	Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr19:51897000-51898800	Flanking Active TSS	Fetal Thymus	thymus

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