Variant report

Variant	rs310475
Chromosome Location	chr19:56153868-56153869
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	chr19:56151221-56155795	A549	lung:	n/a	chr19:56155426-56155435 chr19:56151539-56151548 chr19:56151539-56151549 chr19:56151539-56151549 chr19:56155425-56155436 chr19:56151538-56151549
2	POLR2A	chr19:56151273-56155759	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr19:56150319-56156666	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr19:56153854-56155136	A549	lung:	n/a	n/a
5	POLR2A	chr19:56150228-56156269	GM12891	blood:	n/a	n/a
6	ELF1	chr19:56153367-56153964	A549	lung:	n/a	n/a
7	POLR2A	chr19:56150192-56156534	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:56153839-56155319	A549	lung:	n/a	n/a
9	POLR2A	chr19:56153478-56155220	A549	lung:	n/a	n/a
10	POLR2A	chr19:56153442-56155799	K562	blood:	n/a	n/a
11	POLR2A	chr19:56153630-56153946	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr19:56153525-56155261	MCF-7	breast:	n/a	n/a
13	HMGN3	chr19:56153824-56154548	K562	blood:	n/a	n/a
14	CHD2	chr19:56151532-56155316	Hela-S3	cervix:	n/a	chr19:56154963-56154973 chr19:56152366-56152373
15	POLR2A	chr19:56149778-56157300	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr19:56153491-56155368	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr19:56153814-56155640	HCT-116	colon:	n/a	chr19:56155426-56155435 chr19:56155425-56155436
18	BCL3	chr19:56151732-56155150	A549	lung:	n/a	chr19:56153847-56153856 chr19:56152354-56152363 chr19:56152485-56152494
19	POLR2A	chr19:56150010-56156634	MCF10A-Er-Src	breast:	n/a	n/a
20	HEY1	chr19:56153592-56154046	HepG2	liver:	n/a	n/a
21	POLR2A	chr19:56151299-56155891	MCF-7	breast:	n/a	n/a
22	STAT5A	chr19:56153609-56153919	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:56153835-56153943	A549	lung:	n/a	n/a
24	POLR2A	chr19:56151325-56156943	GM19099	blood:	n/a	n/a
25	POLR2A	chr19:56150270-56155844	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr19:56151350-56155716	GM18526	blood:	n/a	n/a
27	POLR2A	chr19:56153363-56155275	ECC-1	luminal epithelium:	n/a	n/a
28	POLR2A	chr19:56151378-56156635	GM18951	blood:	n/a	n/a
29	POLR2A	chr19:56151603-56155613	U87	brain:	n/a	n/a
30	POLR2A	chr19:56151310-56156615	Raji	blood:	n/a	n/a
31	POLR2A	chr19:56146066-56155822	MCF10A-Er-Src	breast:	n/a	n/a
32	POLR2A	chr19:56153550-56155790	K562	blood:	n/a	n/a
33	POLR2A	chr19:56151262-56156558	GM12878	blood:	n/a	n/a
34	POLR2A	chr19:56150509-56155890	PBDE	blood:	n/a	n/a
35	POLR2A	chr19:56151208-56155527	HCT-116	colon:	n/a	n/a
36	NFATC1	chr19:56153395-56155445	GM12878	blood:	n/a	chr19:56153793-56153807
37	POLR2A	chr19:56150387-56157088	GM18505	blood:	n/a	n/a
38	POLR2A	chr19:56151277-56156546	GM15510	blood:	n/a	n/a
39	BCL3	chr19:56151269-56155527	A549	lung:	n/a	chr19:56153847-56153856 chr19:56152354-56152363 chr19:56152485-56152494 chr19:56155304-56155317
40	POLR2A	chr19:56149442-56155618	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:56151284-56157050	GM19193	blood:	n/a	n/a
42	MAX	chr19:56153532-56155791	HepG2	liver:	n/a	chr19:56155426-56155435 chr19:56155425-56155436
43	POLR2A	chr19:56153866-56155242	HCT-116	colon:	n/a	n/a
44	POLR2A	chr19:56153783-56155802	GM12878	blood:	n/a	n/a
45	POLR2A	chr19:56153211-56155620	HepG2	liver:	n/a	n/a
46	TCF12	chr19:56153390-56154047	A549	lung:	n/a	n/a
47	GATA3	chr19:56151707-56153890	A549	lung:	n/a	chr19:56153293-56153303 chr19:56153441-56153451
48	NFATC1	chr19:56151225-56155139	GM12878	blood:	n/a	chr19:56153793-56153807
49	SIN3AK20	chr19:56153837-56155436	MCF-7	breast:	n/a	n/a
50	MAZ	chr19:56151267-56155787	IMR90	lung:	n/a	chr19:56155426-56155435 chr19:56151539-56151548 chr19:56151539-56151549 chr19:56151539-56151549 chr19:56155425-56155436 chr19:56151538-56151549

No.	Distal block	Cell Line	Cell type
1	chr19:56113112..56115949-chr19:56151962..56154337,3	K562	blood:
2	chr19:56107792..56111497-chr19:56151607..56154571,3	MCF-7	breast:
3	chr19:55894292..55897074-chr19:56152142..56154833,2	MCF-7	breast:
4	chr19:56132811..56137423-chr19:56151241..56156557,5	MCF-7	breast:
5	chr19:55964915..55966958-chr19:56152410..56155336,2	K562	blood:
6	chr19:55628447..55630304-chr19:56152037..56154900,2	K562	blood:
7	chr19:56110523..56113100-chr19:56152133..56154992,3	K562	blood:
8	chr19:56110029..56112023-chr19:56153492..56156368,2	K562	blood:
9	chr19:56134500..56138557-chr19:56151822..56155582,4	K562	blood:
10	chr19:55626366..55629144-chr19:56151698..56154505,2	MCF-7	breast:
11	chr19:56133203..56138391-chr19:56150309..56156340,8	K562	blood:
12	chr19:56153424..56156443-chr19:56220513..56224838,3	K562	blood:
13	chr19:56109287..56112853-chr19:56149861..56154883,7	MCF-7	breast:
14	chr19:55996765..55998431-chr19:56152633..56154883,2	MCF-7	breast:
15	chr19:54973325..54975898-chr19:56151644..56153909,2	MCF-7	breast:
16	chr19:56152176..56154153-chr19:56826714..56828246,2	MCF-7	breast:
17	chr19:56115086..56118069-chr19:56150430..56156112,7	MCF-7	breast:
18	chr19:56114376..56117189-chr19:56151962..56154337,3	K562	blood:
19	chr19:55998666..56000299-chr19:56153756..56156154,2	K562	blood:
20	chr19:56152964..56155802-chr19:56186387..56188533,2	MCF-7	breast:
21	chr19:56152467..56154229-chr19:56171336..56173701,2	MCF-7	breast:

Variant related genes	Relation type
ZNF581	TF binding region
ENSG00000200646	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000233493	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000267549	Chromatin interaction
ENSG00000179954	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000125503	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000182909	Chromatin interaction
ENSG00000269574	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs310436	0.84[YRI][hapmap]
rs504850	0.83[YRI][hapmap]
rs8791	0.83[YRI][hapmap]
rs889092	0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv912503	chr19:56149077-56162776	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
9	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs310475	ZNF580	cis	Nerve Tibial	GTEx
rs310475	AURKC	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56151400-56154000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr19:56151400-56154400	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:56151600-56154200	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr19:56151600-56154400	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr19:56151600-56154800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr19:56151600-56155600	Active TSS	Ovary	ovary
7	chr19:56151600-56155800	Active TSS	Fetal Kidney	kidney
8	chr19:56151600-56156000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr19:56151600-56156200	Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr19:56151600-56156200	Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr19:56151800-56154200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:56151800-56154200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr19:56151800-56154200	Active TSS	Esophagus	oesophagus
14	chr19:56151800-56154400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr19:56151800-56154400	Active TSS	Colon Smooth Muscle	Colon
16	chr19:56151800-56154800	Flanking Active TSS	Primary B cells from cord blood	blood
17	chr19:56151800-56155000	Flanking Active TSS	Primary hematopoietic stem cells	blood
18	chr19:56151800-56155000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr19:56151800-56155000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:56151800-56155800	Active TSS	H9 Cell Line	embryonic stem cell
21	chr19:56151800-56156000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr19:56151800-56156000	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr19:56152000-56154000	Active TSS	Left Ventricle	heart
24	chr19:56152000-56154000	Active TSS	Psoas Muscle	Psoas
25	chr19:56152000-56154200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:56152000-56154200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:56152000-56154200	Active TSS	Aorta	Aorta
28	chr19:56152000-56154200	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr19:56152000-56154200	Active TSS	HepG2	liver
30	chr19:56152000-56154200	Active TSS	HSMMtube	muscle
31	chr19:56152000-56154400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:56152000-56154400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:56152000-56155800	Active TSS	H1 Cell Line	embryonic stem cell
34	chr19:56152200-56154000	Active TSS	HSMM	muscle
35	chr19:56152200-56154200	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr19:56152200-56154200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr19:56152200-56154200	Active TSS	Rectal Smooth Muscle	rectum
38	chr19:56152200-56154200	Active TSS	GM12878-XiMat	blood
39	chr19:56152200-56154200	Active TSS	K562	blood
40	chr19:56152200-56154200	Active TSS	NHEK	skin
41	chr19:56152200-56154200	Active TSS	NHLF	lung
42	chr19:56152200-56154400	Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr19:56152200-56154400	Active TSS	NHDF-Ad	bronchial
44	chr19:56152200-56156000	Active TSS	Small Intestine	intestine
45	chr19:56152600-56154000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:56152600-56154000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:56152600-56154400	Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr19:56152600-56154800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr19:56152600-56154800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr19:56152600-56155000	Flanking Active TSS	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links