Variant report

Variant	rs10424579
Chromosome Location	chr19:51841742-51841743
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	ELF1	chr19:51841703-51842137	K562	blood:	n/a	chr19:51841927-51841940
2	E2F6	chr19:51841698-51842434	A549	lung:	n/a	chr19:51842093-51842104
3	TEAD4	chr19:51841692-51842359	K562	blood:	n/a	n/a
4	NR2F2	chr19:51841702-51842273	K562	blood:	n/a	n/a
5	FOSL2	chr19:51841742-51842965	A549	lung:	n/a	chr19:51842877-51842886 chr19:51842453-51842462 chr19:51842826-51842836
6	MAX	chr19:51841727-51842604	K562	blood:	n/a	chr19:51842127-51842137 chr19:51841906-51841913
7	NR2F2	chr19:51841639-51842582	K562	blood:	n/a	n/a
8	MAX	chr19:51841728-51842357	K562	blood:	n/a	chr19:51842127-51842137 chr19:51841906-51841913
9	MXI1	chr19:51841729-51843936	IMR90	lung:	n/a	n/a
10	STAT5A	chr19:51841740-51842337	K562	blood:	n/a	n/a
11	MXI1	chr19:51841395-51844121	SK-N-SH	brain:	n/a	n/a
12	TEAD4	chr19:51841736-51842348	K562	blood:	n/a	n/a
13	MYC	chr19:51841712-51842624	K562	blood:	n/a	chr19:51842127-51842137 chr19:51841906-51841913
14	EGR1	chr19:51841720-51842373	K562	blood:	n/a	chr19:51842210-51842224
15	IRF1	chr19:51841699-51842628	K562	blood:	n/a	chr19:51842448-51842462
16	CEBPB	chr19:51841708-51841943	K562	blood:	n/a	n/a
17	SMC3	chr19:51841562-51843994	SK-N-SH	brain:	n/a	chr19:51843840-51843850 chr19:51842701-51842711
18	MYC	chr19:51841639-51844033	A549	lung:	n/a	chr19:51843203-51843213 chr19:51842127-51842137 chr19:51841906-51841913 chr19:51843926-51843936
19	MAX	chr19:51841660-51844036	A549	lung:	n/a	chr19:51843203-51843213 chr19:51842127-51842137 chr19:51841906-51841913 chr19:51843926-51843936
20	MAX	chr19:51841676-51842418	A549	lung:	n/a	chr19:51842127-51842137 chr19:51841906-51841913
21	CBX3	chr19:51841598-51842726	K562	blood:	n/a	n/a
22	MYC	chr19:51841711-51843928	K562	blood:	n/a	chr19:51843203-51843213 chr19:51842127-51842137 chr19:51841906-51841913
23	CTCF	chr19:51841718-51843203	SK-N-SH	brain:	n/a	chr19:51842691-51842712 chr19:51842697-51842713
24	RAD21	chr19:51841564-51843843	SK-N-SH	brain:	n/a	chr19:51842694-51842713
25	RAD21	chr19:51841642-51842634	HCT-116	colon:	n/a	n/a
26	USF1	chr19:51841714-51842322	K562	blood:	n/a	n/a
27	JUN	chr19:51841266-51844229	K562	blood:	n/a	chr19:51842877-51842886 chr19:51842453-51842462 chr19:51842826-51842836 chr19:51843435-51843444
28	ZBTB7A	chr19:51841718-51842601	K562	blood:	n/a	n/a
29	SIN3AK20	chr19:51841728-51842538	K562	blood:	n/a	n/a
30	CTCF	chr19:51841495-51844609	A549	lung:	n/a	chr19:51843444-51843457 chr19:51842691-51842712 chr19:51842697-51842713 chr19:51843837-51843850
31	CTCF	chr19:51841700-51842849	HCT-116	colon:	n/a	chr19:51842691-51842712 chr19:51842697-51842713
32	BHLHE40	chr19:51841742-51842333	K562	blood:	n/a	n/a
33	TAL1	chr19:51841739-51842307	K562	blood:	n/a	n/a
34	MAX	chr19:51841741-51842687	MCF-7	breast:	n/a	chr19:51842127-51842137 chr19:51841906-51841913

No.	Distal block	Cell Line	Cell type
1	chr19:51841257..51845442-chr19:51896216..51899567,12	K562	blood:
2	chr19:51841684..51842506-chr19:51897336..51897848,2	K562	blood:
3	chr19:51661756..51662526-chr19:51841495..51842430,2	K562	blood:
4	chr19:51841314..51846809-chr19:51868154..51872523,19	K562	blood:
5	chr19:51841175..51847735-chr19:51867771..51872496,21	MCF-7	breast:
6	chr19:51841279..51843677-chr19:51919444..51921911,2	K562	blood:
7	chr19:51841626..51842658-chr19:51941287..51942856,6	MCF-7	breast:
8	chr19:51841483..51843929-chr19:51917621..51920239,2	K562	blood:
9	chr19:51840838..51845657-chr19:51892354..51900411,18	K562	blood:
10	chr19:51841410..51842759-chr19:51910739..51912174,8	K562	blood:
11	chr19:51841590..51847683-chr19:51867906..51872035,11	MCF-7	breast:
12	chr19:51841717..51843747-chr19:51891710..51894546,2	K562	blood:

Variant related genes	Relation type
ENSG00000267905	TF binding region
ENSG00000142512	Chromatin interaction
ENSG00000268889	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000255441	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000262874	Chromatin interaction
ENSG00000269403	Chromatin interaction
ENSG00000105379	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1035454	0.89[EUR][1000 genomes]
rs10414211	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10419062	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11084068	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878664	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12463376	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2011612	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28668475	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34380065	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509528	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7259266	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8105710	0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv1813225	chr19:51821612-51888813	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51831400-51841800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr19:51831600-51841800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:51832400-51841800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr19:51833000-51842000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr19:51833600-51842000	Weak transcription	Brain Substantia Nigra	brain
6	chr19:51834200-51842200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr19:51834400-51841800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr19:51834600-51841800	Weak transcription	Fetal Intestine Large	intestine
9	chr19:51834800-51841800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr19:51834800-51842000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:51834800-51842200	Weak transcription	Gastric	stomach
12	chr19:51834800-51842200	Weak transcription	Pancreas	Pancrea
13	chr19:51835000-51841800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:51835000-51841800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:51835000-51841800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr19:51835000-51842200	Weak transcription	Left Ventricle	heart
17	chr19:51835600-51841800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr19:51835600-51841800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr19:51835600-51841800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr19:51835800-51841800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:51835800-51841800	Weak transcription	Liver	Liver
22	chr19:51835800-51841800	Weak transcription	Fetal Intestine Small	intestine
23	chr19:51835800-51842200	Weak transcription	Aorta	Aorta
24	chr19:51836000-51841800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:51836000-51842000	Weak transcription	Brain Hippocampus Middle	brain
26	chr19:51836000-51842000	Weak transcription	Ovary	ovary
27	chr19:51836200-51842000	Weak transcription	HepG2	liver
28	chr19:51837600-51841800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr19:51837600-51841800	Weak transcription	A549	lung
30	chr19:51837600-51842200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:51838800-51841800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr19:51838800-51841800	Weak transcription	Brain Germinal Matrix	brain
33	chr19:51839200-51841800	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:51839400-51841800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr19:51840800-51842000	Weak transcription	Esophagus	oesophagus
36	chr19:51841200-51841800	Enhancers	H1 Cell Line	embryonic stem cell
37	chr19:51841200-51841800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:51841200-51842000	Enhancers	Primary hematopoietic stem cells	blood
39	chr19:51841200-51842200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:51841200-51842200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:51841400-51841800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr19:51841400-51841800	Enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr19:51841400-51841800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr19:51841400-51841800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:51841400-51841800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr19:51841400-51842000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:51841400-51842000	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr19:51841400-51842000	Enhancers	Fetal Thymus	thymus
49	chr19:51841400-51842000	Flanking Active TSS	K562	blood
50	chr19:51841600-51841800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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