Variant report

Variant	rs1169076
Chromosome Location	chr12:122429484-122429485
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122429414..122431335-chr12:122431461..122433062,2	MCF-7	breast:
2	chr12:122427530..122430747-chr12:122431781..122435522,3	MCF-7	breast:
3	chr12:122427709..122429547-chr12:122437047..122438935,2	MCF-7	breast:
4	chr12:122428522..122431508-chr12:122460147..122462626,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158023	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1169081	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs1169083	0.95[ASN][1000 genomes]
rs1169084	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1169086	0.94[ASN][1000 genomes]
rs1169087	0.94[ASN][1000 genomes]
rs1169091	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs1177588	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1179947	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1184893	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12578258	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12579389	0.84[ASN][1000 genomes]
rs1375653	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1375654	0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1375655	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1630699	0.80[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1667586	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1678952	0.85[CEU][hapmap];0.87[CHB][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1678953	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1678970	0.84[ASN][1000 genomes]
rs1720030	0.81[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1720035	0.88[TSI][hapmap]
rs1720068	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs17852561	0.85[ASN][1000 genomes]
rs1814592	0.94[ASN][1000 genomes]
rs2009257	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2018749	0.81[ASN][1000 genomes]
rs2272133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2272135	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap]
rs2309275	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs2688411	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2922797	0.81[ASN][1000 genomes]
rs2948663	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35252940	0.83[ASN][1000 genomes]
rs55929316	0.82[ASN][1000 genomes]
rs59972569	0.84[ASN][1000 genomes]
rs658957	0.81[ASN][1000 genomes]
rs686220	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7313748	0.87[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs745327	0.87[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs830115	0.92[ASN][1000 genomes]
rs830118	0.81[ASN][1000 genomes]
rs830120	0.82[CEU][hapmap];0.85[GIH][hapmap]
rs830121	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs895960	0.88[TSI][hapmap]

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	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv899568	chr12:122254713-122456524	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1169076	MSI1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122394000-122429800	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:122396600-122439200	Weak transcription	Brain Anterior Caudate	brain
3	chr12:122412800-122430600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr12:122415200-122434800	Weak transcription	Pancreas	Pancrea
5	chr12:122418800-122437600	Weak transcription	Spleen	Spleen
6	chr12:122419800-122429800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:122422200-122429800	Weak transcription	Thymus	Thymus
8	chr12:122422800-122442600	Weak transcription	Fetal Kidney	kidney
9	chr12:122427600-122429800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:122427800-122430800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:122428200-122430200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:122428200-122430800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:122428200-122430800	Enhancers	NHDF-Ad	bronchial
14	chr12:122428200-122431000	Enhancers	Fetal Thymus	thymus
15	chr12:122428200-122431000	Enhancers	HMEC	breast
16	chr12:122428400-122429800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr12:122428400-122430800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:122428400-122430800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:122428400-122430800	Enhancers	NHEK	skin
20	chr12:122428400-122431000	Enhancers	Primary B cells from peripheral blood	blood
21	chr12:122428600-122429600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:122428600-122430200	Flanking Active TSS	GM12878-XiMat	blood
23	chr12:122428600-122430800	Enhancers	NHLF	lung
24	chr12:122428800-122429800	Enhancers	HSMM	muscle
25	chr12:122428800-122430000	Enhancers	HSMMtube	muscle
26	chr12:122428800-122430000	Enhancers	Osteobl	bone
27	chr12:122428800-122431000	Enhancers	Primary hematopoietic stem cells	blood
28	chr12:122429200-122430000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:122429200-122430000	Enhancers	A549	lung
30	chr12:122429200-122430000	Bivalent Enhancer	HepG2	liver
31	chr12:122429200-122430800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr12:122429200-122431000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:122429200-122431000	Enhancers	NH-A	brain
34	chr12:122429400-122433800	Weak transcription	Fetal Lung	lung

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