Variant report

Variant	rs17074987
Chromosome Location	chr13:51491962-51491963
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
ENSG00000233672	Chromatin interaction
ENSG00000136104	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs2038718	0.85[YRI][hapmap]
rs2274069	0.91[ASN][1000 genomes]
rs4941677	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941678	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4942943	0.92[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59310144	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561599	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs6561601	0.84[ASW][hapmap];0.84[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.87[TSI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6561602	0.91[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.85[YRI][hapmap];0.89[ASN][1000 genomes]
rs6561603	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs730076	0.85[YRI][hapmap]
rs7316955	0.96[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7317618	0.86[CHD][hapmap]
rs7321027	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7324232	0.84[ASW][hapmap];0.84[CEU][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.88[TSI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7329171	0.88[CHD][hapmap];0.85[YRI][hapmap]
rs7988945	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316512	0.85[YRI][hapmap]
rs9535523	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9535526	0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9535534	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17074987	RNASEH2B	cis	Esophagus Muscularis	GTEx
rs17074987	RNASEH2B	cis	Muscle Skeletal	GTEx
rs17074987	RNASEH2B	cis	Artery Tibial	GTEx

Chromatin state (count:92 , 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	chr13:51486800-51495600	Weak transcription	Fetal Intestine Small	intestine
7	chr13:51487000-51498400	Weak transcription	Fetal Stomach	stomach
8	chr13:51487400-51493800	Genic enhancers	Fetal Thymus	thymus
9	chr13:51488400-51492200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr13:51488400-51492200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr13:51488400-51494600	Enhancers	Primary T killer memory cells from peripheral blood	blood
12	chr13:51488400-51496200	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr13:51488600-51493600	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr13:51488600-51493600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr13:51488600-51494200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr13:51488800-51492200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr13:51488800-51492400	Enhancers	Fetal Lung	lung
18	chr13:51488800-51493600	Enhancers	Brain Germinal Matrix	brain
19	chr13:51489200-51492000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr13:51489200-51492200	Enhancers	Adipose Nuclei	Adipose
21	chr13:51489200-51493600	Enhancers	Stomach Smooth Muscle	stomach
22	chr13:51489200-51493800	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr13:51489600-51492200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr13:51489600-51496000	Weak transcription	HSMM	muscle
25	chr13:51489600-51496400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr13:51489600-51496400	Weak transcription	Fetal Kidney	kidney
27	chr13:51489600-51508200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr13:51489800-51496000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr13:51490000-51496400	Weak transcription	Aorta	Aorta
30	chr13:51490400-51492000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr13:51490400-51492000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr13:51490400-51492000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr13:51490600-51492000	Enhancers	Colonic Mucosa	Colon
34	chr13:51490600-51492200	Enhancers	H9 Cell Line	embryonic stem cell
35	chr13:51490600-51492200	Enhancers	Placenta	Placenta
36	chr13:51490600-51492200	Enhancers	Spleen	Spleen
37	chr13:51490600-51492400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr13:51490600-51493000	Enhancers	Right Atrium	heart
39	chr13:51490600-51493600	Enhancers	Colon Smooth Muscle	Colon
40	chr13:51490600-51494200	Enhancers	Brain Hippocampus Middle	brain
41	chr13:51490800-51492000	Enhancers	Pancreas	Pancrea
42	chr13:51490800-51492000	Enhancers	Stomach Mucosa	stomach
43	chr13:51490800-51492400	Enhancers	Lung	lung
44	chr13:51490800-51494400	Enhancers	Brain Anterior Caudate	brain
45	chr13:51491000-51492000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:51491000-51492000	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr13:51491000-51492200	Enhancers	Fetal Muscle Leg	muscle
48	chr13:51491000-51492200	Enhancers	Gastric	stomach
49	chr13:51491000-51492400	Enhancers	Left Ventricle	heart
50	chr13:51491000-51493800	Enhancers	Right Ventricle	heart

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