Variant report

Variant	rs73613271
Chromosome Location	chr19:56189867-56189868
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	MAX	chr19:56188980-56189880	GM12878	blood:	n/a	n/a
2	NFATC1	chr19:56189221-56189979	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:56188862-56190244	GM12892	blood:	n/a	n/a
4	RELA	chr19:56189204-56189973	GM19099	blood:	n/a	n/a
5	IRF4	chr19:56189360-56189958	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:56189275-56190078	GM18951	blood:	n/a	n/a
7	ZEB1	chr19:56189417-56189960	GM12878	blood:	n/a	chr19:56189433-56189444
8	POLR2A	chr19:56189119-56189874	PANC-1	pancreas:	n/a	n/a
9	RELA	chr19:56189378-56190170	GM18951	blood:	n/a	n/a
10	RCOR1	chr19:56189174-56189945	GM12878	blood:	n/a	n/a
11	STAT3	chr19:56189404-56189871	GM12878	blood:	n/a	chr19:56189741-56189752
12	EBF1	chr19:56189156-56190117	GM12878	blood:	n/a	chr19:56189317-56189328
13	POLR2A	chr19:56189337-56190216	K562	blood:	n/a	n/a
14	POLR2A	chr19:56189328-56190197	GM12891	blood:	n/a	n/a
15	SPI1	chr19:56189377-56190031	GM12891	blood:	n/a	chr19:56189741-56189750 chr19:56189488-56189501
16	MTA3	chr19:56189482-56189926	GM12878	blood:	n/a	n/a
17	EP300	chr19:56189537-56189941	GM12878	blood:	n/a	n/a
18	SPI1	chr19:56189013-56190359	GM12878	blood:	n/a	chr19:56189228-56189241 chr19:56190321-56190330 chr19:56189741-56189750 chr19:56189488-56189501
19	EBF1	chr19:56189153-56189888	GM12878	blood:	n/a	chr19:56189317-56189328
20	RAD21	chr19:56189281-56189887	GM12878	blood:	n/a	n/a
21	ELF1	chr19:56189302-56190359	GM12878	blood:	n/a	n/a
22	CTCF	chr19:56189826-56189937	GM19239	blood:	n/a	n/a
23	MXI1	chr19:56188980-56189936	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:56189410-56189876	GM12891	blood:	n/a	n/a
25	RELA	chr19:56189254-56190003	GM18505	blood:	n/a	n/a
26	RUNX3	chr19:56189092-56190042	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:56188478-56190026	GM12891	blood:	n/a	n/a
28	IRF4	chr19:56189397-56190030	GM12878	blood:	n/a	n/a
29	CHD1	chr19:56188894-56190129	GM12878	blood:	n/a	n/a
30	YY1	chr19:56189388-56190088	GM12892	blood:	n/a	n/a
31	SMC3	chr19:56189430-56189943	GM12878	blood:	n/a	n/a
32	BCL11A	chr19:56189486-56189918	GM12878	blood:	n/a	chr19:56189741-56189750
33	SPI1	chr19:56189399-56189956	GM12878	blood:	n/a	chr19:56189741-56189750 chr19:56189488-56189501
34	POLR2A	chr19:56188967-56190097	GM19099	blood:	n/a	n/a
35	POLR2A	chr19:56188228-56190484	GM18505	blood:	n/a	n/a
36	TCF12	chr19:56189574-56189915	GM12878	blood:	n/a	n/a
37	CTCF	chr19:56189834-56189937	GM19240	blood:	n/a	n/a
38	POLR2A	chr19:56189196-56190384	GM12878	blood:	n/a	n/a
39	BHLHE40	chr19:56188930-56190213	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:56189386-56190056	GM12878	blood:	n/a	n/a
41	EP300	chr19:56189482-56189896	GM12878	blood:	n/a	n/a
42	YY1	chr19:56189385-56189881	GM12878	blood:	n/a	n/a
43	PAX5	chr19:56189373-56190135	GM12878	blood:	n/a	chr19:56189741-56189750
44	PML	chr19:56189475-56189894	GM12878	blood:	n/a	n/a
45	RELA	chr19:56189344-56190116	GM19193	blood:	n/a	n/a
46	SP1	chr19:56189277-56190024	GM12878	blood:	n/a	n/a
47	NFIC	chr19:56189421-56189950	GM12878	blood:	n/a	n/a
48	MAZ	chr19:56189443-56189908	GM12878	blood:	n/a	n/a
49	CEBPB	chr19:56189147-56189891	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:56189335-56190022	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
2	chr19:56189741..56193540-chr19:56204383..56209311,7	K562	blood:
3	chr19:56185642..56190165-chr19:56193908..56196750,4	MCF-7	breast:
4	chr19:56188015..56189897-chr19:56203911..56206682,2	MCF-7	breast:
5	chr19:56172318..56174905-chr19:56187838..56190897,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267523	TF binding region
EPN1	TF binding region
ENSG00000063244	Chromatin interaction
ENSG00000211571	Chromatin interaction
ENSG00000203305	Chromatin interaction
ENSG00000267018	Chromatin interaction
ENSG00000267183	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000267117	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs507498	0.96[AFR][1000 genomes]
rs57728680	1.00[AMR][1000 genomes]
rs59066458	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59103531	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59221728	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59316024	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59565463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60314355	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60831229	1.00[AMR][1000 genomes]
rs61540783	1.00[AMR][1000 genomes]
rs7256736	1.00[AMR][1000 genomes]
rs73613277	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73613287	0.98[AFR][1000 genomes]
rs73613290	1.00[AMR][1000 genomes]
rs73613291	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73615028	1.00[AMR][1000 genomes]
rs73615038	1.00[AMR][1000 genomes]
rs73615044	1.00[AMR][1000 genomes]
rs73615090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

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	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
6	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
8	nsv522559	chr19:56185250-56190815	Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 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	chr19:56187200-56190000	Flanking Active TSS	Liver	Liver
2	chr19:56187200-56190000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
3	chr19:56187600-56190200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:56187600-56190600	Genic enhancers	Fetal Muscle Leg	muscle
5	chr19:56187600-56190800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:56187800-56190200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr19:56187800-56192400	Genic enhancers	Placenta	Placenta
8	chr19:56188000-56190000	Enhancers	Primary hematopoietic stem cells	blood
9	chr19:56188000-56190000	Weak transcription	Fetal Kidney	kidney
10	chr19:56188000-56192400	Genic enhancers	Fetal Muscle Trunk	muscle
11	chr19:56188200-56192200	Genic enhancers	Esophagus	oesophagus
12	chr19:56188200-56192800	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr19:56188200-56218200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr19:56188400-56190000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:56188400-56190000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
16	chr19:56188400-56191600	Genic enhancers	Lung	lung
17	chr19:56188400-56192000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:56188400-56192200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr19:56188400-56193200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:56188400-56193800	Strong transcription	Brain Cingulate Gyrus	brain
21	chr19:56188400-56194000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:56188400-56195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr19:56188400-56211200	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr19:56188400-56213600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:56188600-56190200	Enhancers	Colon Smooth Muscle	Colon
26	chr19:56188600-56190400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:56188600-56192800	Genic enhancers	Gastric	stomach
28	chr19:56188600-56193000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
29	chr19:56188600-56194000	Strong transcription	A549	lung
30	chr19:56188600-56210000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr19:56188600-56212400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr19:56188600-56215600	Weak transcription	Fetal Brain Male	brain
33	chr19:56188800-56190200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:56188800-56190600	Genic enhancers	Brain Hippocampus Middle	brain
35	chr19:56188800-56190600	Weak transcription	NH-A	brain
36	chr19:56188800-56191000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr19:56188800-56192800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:56188800-56194000	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr19:56188800-56199800	Weak transcription	HSMMtube	muscle
40	chr19:56188800-56212400	Strong transcription	Thymus	Thymus
41	chr19:56189000-56190000	Weak transcription	HMEC	breast
42	chr19:56189000-56190200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr19:56189000-56190600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr19:56189000-56191000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:56189000-56192200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr19:56189000-56192600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
47	chr19:56189000-56193400	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:56189000-56193400	Genic enhancers	Spleen	Spleen
49	chr19:56189000-56199600	Strong transcription	Fetal Stomach	stomach
50	chr19:56189000-56210000	Strong transcription	Fetal Brain Female	brain

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