Variant report

Variant	rs7508570
Chromosome Location	chr19:51894417-51894418
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	MYC	chr19:51894308-51894676	K562	blood:	n/a	n/a
2	ELF1	chr19:51893625-51894700	K562	blood:	n/a	chr19:51894151-51894164
3	IRF1	chr19:51893820-51894914	K562	blood:	n/a	chr19:51893857-51893871 chr19:51893884-51893898
4	UBTF	chr19:51894399-51894559	K562	blood:	n/a	n/a
5	TAF1	chr19:51893628-51894437	K562	blood:	n/a	n/a
6	EP300	chr19:51893647-51894676	K562	blood:	n/a	n/a
7	POLR2A	chr19:51893611-51894582	K562	blood:	n/a	n/a
8	ZBTB7A	chr19:51893628-51894642	K562	blood:	n/a	chr19:51893821-51893829
9	GABPA	chr19:51893922-51894533	K562	blood:	n/a	n/a
10	POLR2A	chr19:51893574-51894505	K562	blood:	n/a	n/a
11	IRF1	chr19:51893672-51894536	K562	blood:	n/a	chr19:51893857-51893871 chr19:51893884-51893898
12	ZBTB7A	chr19:51893583-51894672	K562	blood:	n/a	chr19:51893821-51893829
13	POLR2A	chr19:51893569-51894644	K562	blood:	n/a	n/a
14	POLR2A	chr19:51893711-51894680	K562	blood:	n/a	n/a
15	HEY1	chr19:51893572-51894687	K562	blood:	n/a	n/a
16	TEAD4	chr19:51893556-51894601	K562	blood:	n/a	n/a
17	ZC3H11A	chr19:51894248-51894439	K562	blood:	n/a	n/a
18	POLR2A	chr19:51893610-51894575	K562	blood:	n/a	n/a
19	POLR2A	chr19:51893476-51894707	K562	blood:	n/a	n/a
20	CUX1	chr19:51894247-51894765	K562	blood:	n/a	n/a
21	POLR2A	chr19:51893602-51894691	K562	blood:	n/a	n/a
22	ELF1	chr19:51893620-51894580	GM12878	blood:	n/a	chr19:51894151-51894164
23	ELF1	chr19:51893925-51894563	GM12878	blood:	n/a	chr19:51894151-51894164
24	RCOR1	chr19:51894296-51894698	K562	blood:	n/a	n/a
25	RCOR1	chr19:51893664-51894795	K562	blood:	n/a	n/a
26	JUND	chr19:51894317-51894888	K562	blood:	n/a	n/a
27	NR2F2	chr19:51893568-51894732	K562	blood:	n/a	n/a
28	ZNF263	chr19:51893829-51894442	K562	blood:	n/a	n/a
29	ELF1	chr19:51893674-51894655	K562	blood:	n/a	chr19:51894151-51894164
30	IRF1	chr19:51893687-51894970	K562	blood:	n/a	chr19:51893857-51893871 chr19:51893884-51893898
31	MAZ	chr19:51893591-51894703	K562	blood:	n/a	n/a
32	POLR2A	chr19:51893515-51894679	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51841717..51843747-chr19:51891710..51894546,2	K562	blood:
2	chr19:51840838..51845657-chr19:51892354..51900411,18	K562	blood:
3	chr19:51867772..51875803-chr19:51892381..51899756,21	K562	blood:
4	chr19:51889349..51894566-chr19:51895156..51899826,6	K562	blood:
5	chr19:51864453..51872845-chr19:51892428..51902096,29	K562	blood:
6	chr19:51889722..51893942-chr19:51894149..51900029,8	K562	blood:

Variant related genes	Relation type
ENSG00000268889	TF binding region
C19orf84	TF binding region
LIM2	TF binding region
ENSG00000105379	Chromatin interaction
ENSG00000269403	Chromatin interaction
ENSG00000268889	Chromatin interaction
ENSG00000268520	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000186806	Chromatin interaction
ENSG00000105370	Chromatin interaction
ENSG00000105374	Chromatin interaction
ENSG00000267905	Chromatin interaction
ENSG00000262874	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10403762	0.81[ASN][1000 genomes]
rs10404198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10419880	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11084075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11669975	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11670065	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11673263	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2411321	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2411322	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2547308	0.96[ASN][1000 genomes]
rs2547309	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2741240	0.92[ASN][1000 genomes]
rs2741241	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3810093	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3810094	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3810095	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3810096	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3810097	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826657	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826658	0.97[ASN][1000 genomes]
rs3826659	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3826660	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826662	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3826663	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826664	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3826665	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4377257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4441376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250926	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7251238	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7251286	0.82[EUR][1000 genomes]
rs7251311	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7251566	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7257275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100861	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8104425	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8107533	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7508570	CTD-2616J11.4	cis	Whole Blood	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51872000-51897000	Weak transcription	Right Atrium	heart
2	chr19:51889200-51897000	Weak transcription	Spleen	Spleen
3	chr19:51891000-51897000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr19:51891600-51897000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:51891800-51897000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr19:51891800-51897000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:51891800-51897000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:51892600-51894800	Active TSS	Fetal Intestine Small	intestine
9	chr19:51892600-51897000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:51893000-51894800	Enhancers	HepG2	liver
11	chr19:51893600-51894600	Active TSS	H9 Cell Line	embryonic stem cell
12	chr19:51893600-51894600	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr19:51893600-51894600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr19:51893600-51894600	Enhancers	Primary B cells from peripheral blood	blood
15	chr19:51893600-51894600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr19:51893600-51894800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr19:51893600-51894800	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr19:51893600-51894800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:51893600-51894800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:51893800-51894600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:51893800-51894800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr19:51894000-51894600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr19:51894000-51894600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr19:51894000-51894600	Enhancers	Esophagus	oesophagus
25	chr19:51894000-51894600	Flanking Active TSS	Fetal Intestine Large	intestine
26	chr19:51894000-51894600	Flanking Active TSS	GM12878-XiMat	blood
27	chr19:51894200-51894600	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr19:51894200-51894600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr19:51894200-51894600	Enhancers	Fetal Muscle Trunk	muscle
30	chr19:51894200-51894600	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr19:51894200-51894600	Enhancers	Thymus	Thymus
32	chr19:51894200-51894800	Enhancers	Primary T cells fromperipheralblood	blood
33	chr19:51894200-51895000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr19:51894200-51896800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:51894200-51897000	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr19:51894200-51897000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:51894200-51897000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr19:51894200-51897000	Weak transcription	Placenta	Placenta
39	chr19:51894200-51897000	Weak transcription	Fetal Stomach	stomach
40	chr19:51894400-51894600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr19:51894400-51894600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr19:51894400-51894600	Enhancers	Primary B cells from cord blood	blood
43	chr19:51894400-51894600	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr19:51894400-51894600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:51894400-51894600	Enhancers	Fetal Lung	lung
46	chr19:51894400-51894800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr19:51894400-51894800	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr19:51894400-51895000	Enhancers	Fetal Thymus	thymus
49	chr19:51894400-51895000	Flanking Active TSS	K562	blood
50	chr19:51894400-51896800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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