Variant report

Variant	rs11617366
Chromosome Location	chr13:51491209-51491210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:51481922..51486486-chr13:51489921..51494512,7	MCF-7	breast:
2	chr13:51483191..51486510-chr13:51488472..51491289,4	MCF-7	breast:
3	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: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10400653	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1041017	0.83[ASW][hapmap];0.87[LWK][hapmap];0.83[AFR][1000 genomes]
rs11616524	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17075018	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17075030	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67932352	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73186365	1.00[ASN][1000 genomes]
rs73186367	1.00[ASN][1000 genomes]
rs73186368	1.00[ASN][1000 genomes]
rs73186369	1.00[ASN][1000 genomes]
rs73186371	1.00[ASN][1000 genomes]
rs73186372	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73186374	1.00[ASN][1000 genomes]
rs73186376	1.00[ASN][1000 genomes]
rs73186381	1.00[ASN][1000 genomes]
rs73186382	1.00[ASN][1000 genomes]
rs73186390	1.00[ASN][1000 genomes]
rs7331290	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7999515	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316511	0.81[CHD][hapmap]
rs9535529	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535531	1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs9535533	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535538	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];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
rs11617366	RNASEH2B	cis	parietal	SCAN
rs11617366	RNASEH2B	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

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	chr13:51486400-51491400	Weak transcription	Brain Substantia Nigra	brain
6	chr13:51486400-51491600	Transcr. at gene 5' and 3'	Dnd41	blood
7	chr13:51486600-51528400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr13:51486800-51491400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr13:51486800-51491600	Weak transcription	HepG2	liver
10	chr13:51486800-51491800	Weak transcription	Brain Angular Gyrus	brain
11	chr13:51486800-51495600	Weak transcription	Fetal Intestine Small	intestine
12	chr13:51487000-51498400	Weak transcription	Fetal Stomach	stomach
13	chr13:51487400-51493800	Genic enhancers	Fetal Thymus	thymus
14	chr13:51488400-51491600	Enhancers	K562	blood
15	chr13:51488400-51492200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr13:51488400-51492200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr13:51488400-51494600	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr13:51488400-51496200	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr13:51488600-51491800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr13:51488600-51493600	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr13:51488600-51493600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr13:51488600-51494200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr13:51488800-51492200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr13:51488800-51492400	Enhancers	Fetal Lung	lung
25	chr13:51488800-51493600	Enhancers	Brain Germinal Matrix	brain
26	chr13:51489200-51491600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr13:51489200-51492000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr13:51489200-51492200	Enhancers	Adipose Nuclei	Adipose
29	chr13:51489200-51493600	Enhancers	Stomach Smooth Muscle	stomach
30	chr13:51489200-51493800	Enhancers	Duodenum Smooth Muscle	Duodenum
31	chr13:51489400-51491400	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr13:51489400-51491400	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr13:51489400-51491600	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr13:51489600-51491400	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr13:51489600-51491600	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr13:51489600-51492200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr13:51489600-51496000	Weak transcription	HSMM	muscle
38	chr13:51489600-51496400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr13:51489600-51496400	Weak transcription	Fetal Kidney	kidney
40	chr13:51489600-51508200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr13:51489800-51491400	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr13:51489800-51496000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr13:51490000-51496400	Weak transcription	Aorta	Aorta
44	chr13:51490400-51492000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr13:51490400-51492000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr13:51490400-51492000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr13:51490600-51491400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr13:51490600-51491400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr13:51490600-51491400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr13:51490600-51491400	Genic enhancers	Fetal Intestine Large	intestine

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