Variant report

Variant	rs12278828
Chromosome Location	chr11:16983627-16983628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:16981957..16983634-chr11:17005634..17007658,3	MCF-7	breast:
2	chr11:16978286..16981863-chr11:16983113..16986432,3	K562	blood:
3	chr11:16983037..16985172-chr11:16987078..16988742,2	MCF-7	breast:
4	chr11:16975638..16979707-chr11:16982694..16985336,3	MCF-7	breast:
5	chr11:16983360..16985149-chr11:16987896..16990823,2	MCF-7	breast:
6	chr11:16981332..16983715-chr11:17008993..17011024,2	MCF-7	breast:
7	chr11:16981822..16987249-chr11:17034138..17037422,6	MCF-7	breast:
8	chr11:16975727..16978192-chr11:16983279..16985913,2	MCF-7	breast:
9	chr11:16980989..16984063-chr11:16991605..16994714,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000184669	Chromatin interaction
ENSG00000166689	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11024078	0.95[YRI][hapmap];1.00[EUR][1000 genomes]
rs11024091	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11024092	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12275536	1.00[EUR][1000 genomes]
rs12276960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12278736	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs12280548	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12292955	1.00[EUR][1000 genomes]
rs16933508	1.00[EUR][1000 genomes]
rs16933515	1.00[EUR][1000 genomes]
rs16933529	1.00[EUR][1000 genomes]
rs16933548	1.00[EUR][1000 genomes]
rs16933592	1.00[EUR][1000 genomes]
rs16933661	1.00[EUR][1000 genomes]
rs2190751	1.00[EUR][1000 genomes]
rs4757454	0.87[YRI][hapmap]
rs4757456	0.87[YRI][hapmap]
rs4757457	0.83[YRI][hapmap]
rs56918856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57289260	1.00[EUR][1000 genomes]
rs57818898	1.00[EUR][1000 genomes]
rs58540437	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60553604	1.00[EUR][1000 genomes]
rs60977991	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61129651	1.00[EUR][1000 genomes]
rs61217675	1.00[EUR][1000 genomes]
rs61475718	1.00[EUR][1000 genomes]
rs6486314	1.00[EUR][1000 genomes]
rs6486315	1.00[EUR][1000 genomes]
rs6486316	1.00[EUR][1000 genomes]
rs7102075	0.80[YRI][hapmap];1.00[EUR][1000 genomes]
rs7102357	0.83[YRI][hapmap];1.00[EUR][1000 genomes]
rs7103382	1.00[EUR][1000 genomes]
rs7117859	0.96[YRI][hapmap];1.00[EUR][1000 genomes]
rs7119994	1.00[EUR][1000 genomes]
rs7122601	1.00[EUR][1000 genomes]
rs7129494	1.00[EUR][1000 genomes]
rs73423200	1.00[EUR][1000 genomes]
rs73425209	1.00[EUR][1000 genomes]
rs73425215	1.00[EUR][1000 genomes]
rs73425221	1.00[EUR][1000 genomes]
rs73425302	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73427252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73427255	0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73427263	1.00[EUR][1000 genomes]
rs7927866	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7935333	1.00[EUR][1000 genomes]
rs7939987	0.87[YRI][hapmap]
rs7944088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7946609	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv7689	chr11:16945953-16990852	Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16955600-16991000	Weak transcription	Right Atrium	heart
2	chr11:16968000-16989800	Weak transcription	Esophagus	oesophagus
3	chr11:16968800-16984400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr11:16975400-16990600	Weak transcription	Spleen	Spleen
5	chr11:16978600-16987600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr11:16978600-16988400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:16980200-16983800	Enhancers	HepG2	liver
8	chr11:16981200-16984400	Weak transcription	GM12878-XiMat	blood
9	chr11:16981200-16987800	Weak transcription	Fetal Kidney	kidney
10	chr11:16981400-16989000	Weak transcription	Brain Anterior Caudate	brain
11	chr11:16981800-17002800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr11:16982000-16985000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:16982000-16988200	Weak transcription	Lung	lung
14	chr11:16982200-16987000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr11:16982200-16987600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:16982200-16987800	Weak transcription	Fetal Lung	lung
17	chr11:16982200-16987800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:16982200-16999000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:16982200-17003800	Weak transcription	Right Ventricle	heart
20	chr11:16982400-16984600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr11:16982400-16988200	Weak transcription	Liver	Liver
22	chr11:16982600-16987000	Weak transcription	Pancreas	Pancrea
23	chr11:16982600-16989000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr11:16982800-16985800	Strong transcription	Fetal Intestine Large	intestine
25	chr11:16982800-16987000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr11:16983400-16983800	Weak transcription	Stomach Mucosa	stomach
27	chr11:16983400-16984800	Strong transcription	Fetal Intestine Small	intestine
28	chr11:16983600-16983800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr11:16983600-16983800	Weak transcription	Gastric	stomach

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