Variant report

Variant	rs17589481
Chromosome Location	chr13:51466164-51466165
allele	A/G
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	GATA2	chr13:51466062-51466613	SH-SY5Y	brain:	n/a	chr13:51466385-51466396
2	POLR2A	chr13:51466164-51466803	HL-60	blood:	n/a	n/a
3	POLR2A	chr13:51465521-51468914	GM12891	blood:	n/a	n/a
4	NFIC	chr13:51466161-51467095	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNASEH2B-AS1	TF binding region

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1328360	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1870839	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2441	1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[ASN][1000 genomes]
rs4942941	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994724	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9526704	1.00[ASN][1000 genomes]
rs9526705	1.00[ASN][1000 genomes]
rs9526708	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9535516	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535524	1.00[ASN][1000 genomes]
rs9535525	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9535528	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9535530	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9591369	0.85[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	nsv900077	chr13:51446114-51514831	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv900078	chr13:51454896-51478716	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17589481	CPB2	cis	cerebellum	SCAN
rs17589481	RNASEH2B	cis	Muscle Skeletal	GTEx
rs17589481	RNASEH2B-AS1	cis	Thyroid	GTEx

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51462000-51466200	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr13:51463400-51466400	Enhancers	Primary B cells from peripheral blood	blood
3	chr13:51463600-51466200	Enhancers	Primary T cells from cord blood	blood
4	chr13:51463600-51466200	Enhancers	Primary hematopoietic stem cells	blood
5	chr13:51463800-51467400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:51464200-51466800	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr13:51464200-51466800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr13:51464400-51466200	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr13:51464400-51466400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr13:51464400-51467400	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr13:51464600-51466400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr13:51464600-51467000	Flanking Active TSS	Dnd41	blood
13	chr13:51465000-51466400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr13:51465000-51466400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr13:51465200-51466200	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr13:51465200-51466400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr13:51465200-51466400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr13:51465200-51466400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr13:51465200-51466800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr13:51465400-51466400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr13:51465400-51466600	Flanking Active TSS	GM12878-XiMat	blood
22	chr13:51465400-51466800	Enhancers	Primary T cells fromperipheralblood	blood
23	chr13:51465400-51467200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr13:51465600-51466400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr13:51465600-51466600	Flanking Active TSS	Thymus	Thymus
26	chr13:51465600-51468400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr13:51465600-51474600	Weak transcription	Aorta	Aorta
28	chr13:51465800-51467400	Weak transcription	Duodenum Mucosa	Duodenum
29	chr13:51465800-51468400	Flanking Active TSS	Fetal Thymus	thymus
30	chr13:51466000-51466200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr13:51466000-51467000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
32	chr13:51466000-51467000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr13:51466000-51467200	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr13:51466000-51467600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr13:51466000-51468000	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr13:51466000-51469000	Enhancers	HUES64 Cell Line	embryonic stem cell
37	chr13:51466000-51469000	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr13:51466000-51469200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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