Variant report

Variant	rs59310144
Chromosome Location	chr13:51491780-51491781
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51481922..51486486-chr13:51489921..51494512,7	MCF-7	breast:
2	chr13:51486556..51488218-chr13:51489286..51491989,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136104	Chromatin interaction
ENSG00000233672	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17074987	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274069	0.91[ASN][1000 genomes]
rs4941677	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941678	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4942943	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6561599	0.84[ASN][1000 genomes]
rs6561601	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6561602	0.89[ASN][1000 genomes]
rs6561603	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7316955	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7321027	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7324232	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7988945	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535523	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9535526	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535534	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs59310144	RNASEH2B	cis	Esophagus Muscularis	GTEx
rs59310144	RNASEH2B	cis	Artery Tibial	GTEx
rs59310144	RNASEH2B	cis	Muscle Skeletal	GTEx
rs59310144	RNASEH2B	cis	Thyroid	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51485000-51496200	Weak transcription	Ovary	ovary
2	chr13:51485200-51495600	Weak transcription	Fetal Muscle Trunk	muscle
3	chr13:51485400-51504200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:51486000-51495800	Weak transcription	Fetal Brain Female	brain
5	chr13:51486600-51528400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr13:51486800-51491800	Weak transcription	Brain Angular Gyrus	brain
7	chr13:51486800-51495600	Weak transcription	Fetal Intestine Small	intestine
8	chr13:51487000-51498400	Weak transcription	Fetal Stomach	stomach
9	chr13:51487400-51493800	Genic enhancers	Fetal Thymus	thymus
10	chr13:51488400-51492200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr13:51488400-51492200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr13:51488400-51494600	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr13:51488400-51496200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr13:51488600-51491800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr13:51488600-51493600	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr13:51488600-51493600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr13:51488600-51494200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr13:51488800-51492200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr13:51488800-51492400	Enhancers	Fetal Lung	lung
20	chr13:51488800-51493600	Enhancers	Brain Germinal Matrix	brain
21	chr13:51489200-51492000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr13:51489200-51492200	Enhancers	Adipose Nuclei	Adipose
23	chr13:51489200-51493600	Enhancers	Stomach Smooth Muscle	stomach
24	chr13:51489200-51493800	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr13:51489600-51492200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr13:51489600-51496000	Weak transcription	HSMM	muscle
27	chr13:51489600-51496400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr13:51489600-51496400	Weak transcription	Fetal Kidney	kidney
29	chr13:51489600-51508200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr13:51489800-51496000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr13:51490000-51496400	Weak transcription	Aorta	Aorta
32	chr13:51490400-51492000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
33	chr13:51490400-51492000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr13:51490400-51492000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr13:51490600-51491800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr13:51490600-51491800	Flanking Active TSS	GM12878-XiMat	blood
37	chr13:51490600-51492000	Enhancers	Colonic Mucosa	Colon
38	chr13:51490600-51492200	Enhancers	H9 Cell Line	embryonic stem cell
39	chr13:51490600-51492200	Enhancers	Placenta	Placenta
40	chr13:51490600-51492200	Enhancers	Spleen	Spleen
41	chr13:51490600-51492400	Enhancers	Sigmoid Colon	Sigmoid Colon
42	chr13:51490600-51493000	Enhancers	Right Atrium	heart
43	chr13:51490600-51493600	Enhancers	Colon Smooth Muscle	Colon
44	chr13:51490600-51494200	Enhancers	Brain Hippocampus Middle	brain
45	chr13:51490800-51491800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr13:51490800-51492000	Enhancers	Pancreas	Pancrea
47	chr13:51490800-51492000	Enhancers	Stomach Mucosa	stomach
48	chr13:51490800-51492400	Enhancers	Lung	lung
49	chr13:51490800-51494400	Enhancers	Brain Anterior Caudate	brain
50	chr13:51491000-51492000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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