Variant report

Variant	rs9535530
Chromosome Location	chr13:51499272-51499273
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	SETDB1	chr13:51499144-51499541	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:51488225..51491111-chr13:51497807..51500675,3	K562	blood:
2	chr13:50363476..50366040-chr13:51498906..51500626,2	K562	blood:
3	chr13:51483976..51485601-chr13:51498682..51500533,2	K562	blood:

Variant related genes	Relation type
RNASEH2B	TF binding region
ENSG00000233672	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1328360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17589481	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1870839	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2441	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942941	1.00[ASN][1000 genomes]
rs7994724	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9526704	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526705	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526708	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535516	1.00[ASN][1000 genomes]
rs9535524	1.00[ASN][1000 genomes]
rs9535525	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535528	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535532	0.94[EUR][1000 genomes]
rs9591369	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9535530	RNASEH2B-AS1	cis	Thyroid	GTEx
rs9535530	RNASEH2B	cis	Muscle Skeletal	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51485400-51504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:51486600-51528400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:51489600-51508200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr13:51491600-51551000	Weak transcription	Small Intestine	intestine
5	chr13:51493800-51504800	Weak transcription	Right Ventricle	heart
6	chr13:51494000-51502400	Weak transcription	Fetal Heart	heart
7	chr13:51494800-51500400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr13:51495000-51500400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
9	chr13:51495200-51500200	ZNF genes & repeats	Primary B cells from cord blood	blood
10	chr13:51495200-51500400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
11	chr13:51495600-51500400	ZNF genes & repeats	Primary T cells from cord blood	blood
12	chr13:51495800-51499800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
13	chr13:51496000-51499600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
14	chr13:51496000-51499600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr13:51496000-51499800	ZNF genes & repeats	Fetal Lung	lung
16	chr13:51496600-51503800	Weak transcription	Left Ventricle	heart
17	chr13:51496600-51504200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr13:51496600-51508200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr13:51496600-51529800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr13:51496800-51508600	Weak transcription	Fetal Kidney	kidney
21	chr13:51496800-51510600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr13:51496800-51533200	Weak transcription	NH-A	brain
23	chr13:51497000-51503200	Weak transcription	Thymus	Thymus
24	chr13:51498200-51501600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr13:51498400-51499800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr13:51498400-51508600	Weak transcription	Brain Hippocampus Middle	brain
27	chr13:51498800-51499400	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr13:51499000-51499400	Weak transcription	Dnd41	blood
29	chr13:51499000-51499600	Weak transcription	Fetal Thymus	thymus
30	chr13:51499000-51502600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr13:51499000-51508200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr13:51499000-51509000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr13:51499200-51501400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr13:51499200-51502400	Weak transcription	Primary T cells fromperipheralblood	blood

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