Variant report

Variant	rs10850747
Chromosome Location	chr12:117490510-117490511
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	chr12:117488907..117491503-chr12:117528799..117530966,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10735100	0.83[JPT][hapmap]
rs10735101	0.83[JPT][hapmap]
rs10744887	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10774895	0.82[JPT][hapmap]
rs10774898	0.83[JPT][hapmap]
rs10774899	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10850734	0.83[JPT][hapmap]
rs10850742	0.84[ASN][1000 genomes]
rs10850745	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10850746	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10850751	0.92[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10850752	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11068292	0.81[JPT][hapmap]
rs11068299	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11068300	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11068301	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11068306	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11611741	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832441	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11834817	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11837022	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12368876	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1472523	0.92[CEU][hapmap];0.81[JPT][hapmap];0.85[EUR][1000 genomes]
rs2062528	0.96[CEU][hapmap];0.88[JPT][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2173654	0.92[CEU][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2291911	0.92[CEU][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2291916	0.83[JPT][hapmap]
rs2393124	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3782191	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3782192	0.88[CEU][hapmap];0.93[EUR][1000 genomes]
rs4766816	0.83[JPT][hapmap]
rs4766823	0.83[JPT][hapmap]
rs4766825	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4767477	0.83[JPT][hapmap]
rs55969361	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs58470318	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59756806	0.84[EUR][1000 genomes]
rs6490103	0.82[JPT][hapmap]
rs6490104	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6490105	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490106	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490107	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133090	0.83[JPT][hapmap]
rs7294692	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7297303	0.84[CEU][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7297917	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7486428	0.83[JPT][hapmap]
rs7953553	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7956481	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7960638	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7960731	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7964668	0.96[CEU][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7964686	0.88[CEU][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs7968761	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7968891	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7971795	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7972416	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978810	0.86[CEU][hapmap];0.97[EUR][1000 genomes]
rs9634171	0.96[CEU][hapmap];0.88[JPT][hapmap];0.87[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832524	chr12:117314110-117496576	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv899541	chr12:117414974-117497066	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv1804583	chr12:117472107-117525169	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10850747	TESC	cis	lymphoblastoid	seeQTL
rs10850747	TESC	cis	parietal	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117483800-117498000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:117483800-117498200	Weak transcription	Brain Angular Gyrus	brain
3	chr12:117483800-117498200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:117484000-117490800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr12:117484000-117493600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr12:117484400-117497800	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:117484800-117498200	Weak transcription	Thymus	Thymus
8	chr12:117485800-117490600	Enhancers	K562	blood
9	chr12:117486600-117491000	Weak transcription	Stomach Mucosa	stomach
10	chr12:117486600-117500400	Weak transcription	Fetal Lung	lung
11	chr12:117486800-117491800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr12:117486800-117498800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:117487000-117493400	Weak transcription	Lung	lung
14	chr12:117487200-117492000	Weak transcription	Gastric	stomach
15	chr12:117487200-117500400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:117487400-117490600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr12:117487400-117491000	Weak transcription	Dnd41	blood
18	chr12:117487400-117491400	Weak transcription	Spleen	Spleen
19	chr12:117487400-117494200	Weak transcription	A549	lung
20	chr12:117487400-117497000	Weak transcription	Ovary	ovary
21	chr12:117488200-117491200	Weak transcription	HepG2	liver
22	chr12:117488200-117491400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr12:117488200-117491600	Enhancers	Pancreas	Pancrea
24	chr12:117488400-117490600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
25	chr12:117488400-117491200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:117488400-117491800	Enhancers	Left Ventricle	heart
27	chr12:117488600-117496800	Weak transcription	Right Atrium	heart
28	chr12:117488800-117491000	Bivalent Enhancer	Fetal Muscle Leg	muscle
29	chr12:117488800-117491400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:117488800-117491600	Enhancers	GM12878-XiMat	blood
31	chr12:117488800-117491800	Enhancers	H1 Cell Line	embryonic stem cell
32	chr12:117489000-117491400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr12:117489000-117491400	Weak transcription	Fetal Brain Male	brain
34	chr12:117489000-117492200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:117489200-117491200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
36	chr12:117489200-117491600	Enhancers	Primary B cells from peripheral blood	blood
37	chr12:117489200-117491800	Enhancers	Fetal Thymus	thymus
38	chr12:117489200-117493600	Enhancers	Fetal Heart	heart
39	chr12:117489400-117491000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr12:117489400-117491400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr12:117489400-117491600	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr12:117489600-117490600	Weak transcription	Placenta	Placenta
43	chr12:117489600-117491600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:117489600-117500400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr12:117489800-117490600	Bivalent Enhancer	Fetal Stomach	stomach
46	chr12:117489800-117491000	Enhancers	Brain Germinal Matrix	brain
47	chr12:117489800-117491200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:117489800-117491200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
49	chr12:117489800-117491600	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr12:117489800-117492200	Enhancers	Right Ventricle	heart

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