Variant report

Variant	rs6728168
Chromosome Location	chr2:111472878-111472879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:111471612..111473359-chr2:111497038..111499262,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10175974	1.00[CEU][hapmap]
rs10203271	1.00[CEU][hapmap]
rs11900983	1.00[CEU][hapmap]
rs11903773	1.00[CEU][hapmap]
rs12474907	0.92[EUR][1000 genomes]
rs13386878	1.00[CEU][hapmap]
rs13388313	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs13398617	1.00[CEU][hapmap]
rs13410685	1.00[CEU][hapmap]
rs13415981	1.00[CEU][hapmap]
rs13421709	1.00[EUR][1000 genomes]
rs13426054	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13430683	1.00[CEU][hapmap]
rs17041539	1.00[JPT][hapmap]
rs17041553	1.00[JPT][hapmap]
rs17041555	1.00[JPT][hapmap]
rs17464100	1.00[JPT][hapmap]
rs34026418	1.00[JPT][hapmap]
rs3817265	1.00[JPT][hapmap]
rs4255970	1.00[CEU][hapmap]
rs66616139	1.00[ASN][1000 genomes]
rs6752335	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs68130860	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72828843	0.84[ASN][1000 genomes]
rs72828844	0.84[ASN][1000 genomes]
rs72828845	0.84[ASN][1000 genomes]
rs72828847	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72828848	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72828850	1.00[EUR][1000 genomes]
rs7419932	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7581640	1.00[CEU][hapmap]
rs7592058	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs7609252	1.00[CEU][hapmap]
rs977406	1.00[JPT][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	nsv1008581	chr2:110826262-111487021	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv874838	chr2:111376870-112046226	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv874839	chr2:111400934-111868010	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1008758	chr2:111415136-111626467	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv535890	chr2:111415136-111626467	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6728168	AC013268.5	cis	Artery Aorta	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:111471800-111473200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr2:111471800-111473200	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr2:111472000-111473000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:111472000-111475000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:111472000-111475000	Weak transcription	NHEK	skin
6	chr2:111472200-111473000	Enhancers	Fetal Kidney	kidney
7	chr2:111472200-111473200	Enhancers	Adipose Nuclei	Adipose
8	chr2:111472400-111473000	Enhancers	Liver	Liver
9	chr2:111472400-111473000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr2:111472400-111473600	Enhancers	Ovary	ovary
11	chr2:111472600-111473000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr2:111472600-111473200	Enhancers	GM12878-XiMat	blood
13	chr2:111472600-111473600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr2:111472600-111474600	Weak transcription	HMEC	breast
15	chr2:111472600-111476400	Weak transcription	Placenta	Placenta
16	chr2:111472800-111474600	Weak transcription	Fetal Lung	lung

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