Variant report

Variant	rs12469035
Chromosome Location	chr2:127984917-127984918
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:127983318..127986030-chr2:128006327..128008431,2	MCF-7	breast:
2	chr2:127974300..127976848-chr2:127983797..127985574,2	MCF-7	breast:
3	chr2:127983824..127986072-chr2:128049490..128052043,3	MCF-7	breast:
4	chr2:127978350..127980779-chr2:127984214..127985920,2	MCF-7	breast:
5	chr2:127972542..127975941-chr2:127982453..127985678,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163161	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12463909	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12465955	0.89[EUR][1000 genomes]
rs12623948	0.83[EUR][1000 genomes]
rs1566822	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2174270	0.89[EUR][1000 genomes]
rs2896888	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35328149	0.83[EUR][1000 genomes]
rs3902960	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4150407	0.85[EUR][1000 genomes]
rs4560059	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4580338	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4662710	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4662711	0.82[EUR][1000 genomes]
rs4662712	0.89[EUR][1000 genomes]
rs4662717	0.87[EUR][1000 genomes]
rs55905117	0.82[EUR][1000 genomes]
rs58475809	0.87[EUR][1000 genomes]
rs6430931	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6712213	0.83[EUR][1000 genomes]
rs6712446	0.83[EUR][1000 genomes]
rs6712551	0.83[EUR][1000 genomes]
rs71414745	0.85[EUR][1000 genomes]
rs7585198	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7591760	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9636235	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9636236	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006112	chr2:127830117-128032546	Transcr. at gene 5' and 3' Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2757832	chr2:127830943-128006514	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2759090	chr2:127830943-128006514	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1011378	chr2:127841930-128020546	Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv999809	chr2:127841930-128032546	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1010669	chr2:127848860-128032546	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1003599	chr2:127871183-128059407	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv535920	chr2:127871183-128059407	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127982400-127985000	Flanking Active TSS	Osteobl	bone
2	chr2:127983200-127985000	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr2:127983600-127985000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:127983600-127985000	Enhancers	Liver	Liver
5	chr2:127983800-127985000	Enhancers	Esophagus	oesophagus
6	chr2:127983800-127985000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
7	chr2:127983800-127985000	Enhancers	Stomach Mucosa	stomach
8	chr2:127983800-127985000	Flanking Active TSS	Hela-S3	cervix
9	chr2:127984400-127985000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:127984400-127987800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:127984600-128012800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:127984800-127985000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:127984800-127985000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:127984800-127985000	Enhancers	NHEK	skin
15	chr2:127984800-127985200	Enhancers	A549	lung
16	chr2:127984800-127985800	Enhancers	NH-A	brain
17	chr2:127984800-127986200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:127984800-127988200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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