Variant report

Variant	rs2798724
Chromosome Location	chr9:15401046-15401047
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:15399457..15401521-chr9:15510230..15512381,2	MCF-7	breast:
2	chr9:15305818..15308791-chr9:15400718..15402980,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155158	Chromatin interaction
ENSG00000164985	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10122299	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10125861	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10962020	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2040071	0.96[ASN][1000 genomes]
rs2487860	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488955	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488956	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488960	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2488967	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2488968	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490863	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2798708	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798710	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798711	0.96[ASN][1000 genomes]
rs2798713	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2798714	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2798715	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2798716	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798718	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2798719	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798720	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798721	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798722	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798723	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798741	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798742	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798743	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2804996	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2804997	0.96[ASN][1000 genomes]
rs2805000	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2805004	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2805005	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2805006	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2805007	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28870710	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62573012	0.90[ASN][1000 genomes]
rs6474912	1.00[EUR][1000 genomes];0.99[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	nsv892624	chr9:15283761-15415461	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1030287	chr9:15332709-15458001	Weak transcription Enhancers Strong transcription Active TSS 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	17 gene(s)	inside rSNPs	diseases
5	nsv1032861	chr9:15378192-15410429	Enhancers Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv1022227	chr9:15379786-15416659	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15400000-15401400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr9:15400000-15402000	Enhancers	Fetal Intestine Large	intestine
3	chr9:15400000-15402000	Enhancers	Fetal Intestine Small	intestine
4	chr9:15400200-15401600	Enhancers	Fetal Kidney	kidney
5	chr9:15400200-15402200	Enhancers	Muscle Satellite Cultured Cells	--
6	chr9:15400400-15401400	Enhancers	Osteobl	bone
7	chr9:15400400-15401800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:15400400-15401800	Enhancers	Fetal Lung	lung
9	chr9:15400600-15401400	Enhancers	Hela-S3	cervix
10	chr9:15400600-15402000	Enhancers	NHLF	lung
11	chr9:15400800-15401200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr9:15400800-15401600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:15400800-15401800	Enhancers	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links