Variant report

Variant	rs507498
Chromosome Location	chr19:56171778-56171779
allele	G/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	POLR2A	chr19:56171680-56172521	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr19:56171333-56172215	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:56171693-56172818	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr19:56171601-56171787	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:56171537-56172154	PFSK-1	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56152467..56154229-chr19:56171336..56173701,2	MCF-7	breast:
2	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:

Variant related genes	Relation type
U2AF2	TF binding region
ENSG00000063245	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000267523	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11545669	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310438	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310439	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310442	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310443	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310444	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310464	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs310465	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs310467	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs310470	0.83[EUR][1000 genomes]
rs310471	0.83[EUR][1000 genomes]
rs310474	0.83[EUR][1000 genomes]
rs504003	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs520125	1.00[CHB][hapmap]
rs522669	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs537728	1.00[CEU][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs553947	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs57063593	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581023	1.00[ASN][1000 genomes]
rs59103531	0.83[AFR][1000 genomes]
rs59221728	0.94[AFR][1000 genomes]
rs59316024	0.94[AFR][1000 genomes]
rs59565463	0.96[AFR][1000 genomes]
rs600106	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60314355	0.85[AFR][1000 genomes]
rs612211	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs630491	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636466	0.83[EUR][1000 genomes]
rs636467	0.83[EUR][1000 genomes]
rs637788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs644230	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs679577	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs680444	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246799	0.83[EUR][1000 genomes]
rs73613271	0.96[AFR][1000 genomes]
rs73613277	0.93[AFR][1000 genomes]
rs73613287	0.94[AFR][1000 genomes]
rs73613291	0.94[AFR][1000 genomes]
rs73615090	0.96[AFR][1000 genomes]
rs889091	1.00[CHB][hapmap];1.00[CHD][hapmap]

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	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
5	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
6	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
7	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
8	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56167600-56174200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:56168200-56171800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:56168200-56172400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr19:56168200-56172800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr19:56168600-56172200	Genic enhancers	Spleen	Spleen
6	chr19:56169200-56172200	Genic enhancers	Lung	lung
7	chr19:56169200-56173200	Weak transcription	Fetal Kidney	kidney
8	chr19:56169200-56173600	Genic enhancers	A549	lung
9	chr19:56169400-56171800	Genic enhancers	Pancreas	Pancrea
10	chr19:56169400-56172600	Genic enhancers	Primary T cells fromperipheralblood	blood
11	chr19:56169400-56172600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:56169600-56172000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:56169600-56172200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr19:56169600-56173200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:56169600-56173200	Weak transcription	HSMMtube	muscle
16	chr19:56169600-56181600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:56169800-56171800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr19:56169800-56172600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:56170000-56172000	Weak transcription	HSMM	muscle
20	chr19:56170000-56172200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr19:56170000-56172400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr19:56170000-56173200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
23	chr19:56170000-56181600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:56170000-56181600	Strong transcription	Aorta	Aorta
25	chr19:56170000-56181800	Strong transcription	H9 Cell Line	embryonic stem cell
26	chr19:56170000-56184800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:56170200-56172000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
28	chr19:56170200-56172000	Weak transcription	NH-A	brain
29	chr19:56170200-56172200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr19:56170200-56172200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
31	chr19:56170200-56172200	Genic enhancers	Dnd41	blood
32	chr19:56170200-56172800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
33	chr19:56170200-56173000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr19:56170200-56173200	Weak transcription	NHDF-Ad	bronchial
35	chr19:56170200-56173800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:56170200-56176000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr19:56170200-56178400	Strong transcription	NHEK	skin
38	chr19:56170200-56181600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr19:56170200-56181800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:56170200-56182200	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr19:56170200-56182400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr19:56170200-56182400	Strong transcription	Rectal Smooth Muscle	rectum
43	chr19:56170200-56184000	Strong transcription	Primary T cells from cord blood	blood
44	chr19:56170200-56185200	Strong transcription	Fetal Thymus	thymus
45	chr19:56170200-56185400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr19:56170200-56185800	Strong transcription	Fetal Stomach	stomach
47	chr19:56170400-56171800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:56170400-56172400	Genic enhancers	Stomach Smooth Muscle	stomach
49	chr19:56170400-56177400	Strong transcription	Fetal Intestine Small	intestine
50	chr19:56170400-56179800	Strong transcription	Hela-S3	cervix

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