Variant report

Variant	rs7270971
Chromosome Location	chr20:53223171-53223172
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53221224..53225981-chr20:53225997..53231429,8	MCF-7	breast:
2	chr20:52823473..52826464-chr20:53220337..53223310,3	MCF-7	breast:
3	chr20:53153790..53156293-chr20:53221981..53224189,2	MCF-7	breast:
4	chr20:53219603..53221851-chr20:53222330..53224906,2	MCF-7	breast:
5	chr20:53217074..53219362-chr20:53220946..53223894,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13040265	1.00[CHD][hapmap]
rs13043020	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1569985	1.00[CHD][hapmap]
rs16999830	0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16999872	0.91[CEU][hapmap]
rs1983702	1.00[CHD][hapmap]
rs2054432	0.85[LWK][hapmap];0.89[YRI][hapmap]
rs2180462	1.00[CHD][hapmap]
rs2208075	1.00[CHD][hapmap]
rs2224269	0.91[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2870331	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2870332	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2870333	1.00[CHD][hapmap]
rs2870337	1.00[CHD][hapmap]
rs4302265	1.00[CHD][hapmap]
rs4334548	1.00[CHD][hapmap]
rs4809969	1.00[CHD][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.83[AMR][1000 genomes]
rs4811509	0.83[AMR][1000 genomes]
rs4811512	1.00[CEU][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6014067	0.87[LWK][hapmap];0.86[YRI][hapmap]
rs6014073	0.85[YRI][hapmap]
rs6014076	0.85[LWK][hapmap];0.93[YRI][hapmap]
rs6014078	0.90[YRI][hapmap]
rs6014080	0.90[YRI][hapmap]
rs6014081	1.00[CHD][hapmap]
rs6014106	1.00[CHD][hapmap]
rs6023367	1.00[CHD][hapmap]
rs6023385	0.85[LWK][hapmap]
rs6023387	0.86[YRI][hapmap]
rs6023394	0.83[YRI][hapmap]
rs6023397	0.93[YRI][hapmap]
rs6023398	0.90[YRI][hapmap]
rs6023401	0.90[YRI][hapmap]
rs6023403	0.83[YRI][hapmap]
rs6023406	1.00[CHD][hapmap]
rs6023423	1.00[CHD][hapmap]
rs6023429	1.00[CHD][hapmap]
rs6023430	1.00[CHD][hapmap]
rs6023474	1.00[CHD][hapmap]
rs6064092	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6064093	0.91[CEU][hapmap];1.00[CHD][hapmap]
rs6064102	1.00[CHD][hapmap]
rs6068912	0.95[MEX][hapmap];0.85[MKK][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6068919	0.91[CEU][hapmap]
rs6068920	0.94[CEU][hapmap]
rs6068923	0.89[CEU][hapmap]
rs6068924	1.00[CHD][hapmap]
rs6098108	0.92[CEU][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6098158	1.00[CHD][hapmap]
rs6123404	1.00[CHD][hapmap]
rs6417302	0.82[AMR][1000 genomes]
rs7263678	1.00[CHD][hapmap]
rs7263680	0.91[CEU][hapmap]
rs7269966	0.83[YRI][hapmap]
rs7270451	0.91[CEU][hapmap];1.00[CHD][hapmap]
rs8115071	0.91[CEU][hapmap];1.00[CHD][hapmap]
rs8124702	1.00[CHD][hapmap]
rs910850	1.00[CHD][hapmap]
rs967377	1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv586282	chr20:53218978-53254815	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7270971	RAE1	cis	cerebellum	SCAN
rs7270971	SALL4	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53202200-53230800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:53204600-53240600	Weak transcription	Left Ventricle	heart
3	chr20:53206400-53226600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr20:53215200-53236400	Weak transcription	Aorta	Aorta
5	chr20:53216400-53227000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:53216800-53226800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr20:53217000-53225800	Weak transcription	Fetal Brain Female	brain
8	chr20:53217000-53235800	Weak transcription	Brain Germinal Matrix	brain
9	chr20:53217400-53240600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr20:53217800-53226200	Weak transcription	Fetal Brain Male	brain
11	chr20:53217800-53227000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr20:53217800-53227400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr20:53221600-53239000	Weak transcription	Osteobl	bone
14	chr20:53222400-53225800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr20:53222800-53223600	Enhancers	Primary B cells from peripheral blood	blood
16	chr20:53222800-53224000	Enhancers	GM12878-XiMat	blood
17	chr20:53222800-53225600	Enhancers	Monocytes-CD14+_RO01746	blood

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