Variant report

Variant	rs12520008
Chromosome Location	chr5:17078295-17078296
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	chr5:17068695..17071363-chr5:17076784..17079484,2	MCF-7	breast:
2	chr5:17076577..17078375-chr5:17096009..17098566,2	MCF-7	breast:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10050750	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12109054	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12514216	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12519524	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521131	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13189103	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2086607	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2101149	0.90[ASN][1000 genomes]
rs2128311	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2128312	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2170526	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28412452	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34398449	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34738571	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35725865	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4702194	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6554967	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6863571	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6872871	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6874789	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6889105	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6896287	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025225	chr5:16714512-17234866	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1015247	chr5:16748966-17133274	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv880277	chr5:16829442-17316288	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	esv3510797	chr5:16966764-17125849	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3510798	chr5:16966764-17125849	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv1795984	chr5:16973769-17078295	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv1017222	chr5:17001819-17133274	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1021972	chr5:17011758-17091878	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv1026025	chr5:17039665-17195440	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1027435	chr5:17068441-17095350	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv969212	chr5:17070735-17098476	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:17070600-17079800	Weak transcription	Gastric	stomach
2	chr5:17070600-17080600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:17075000-17079400	Enhancers	HUVEC	blood vessel
4	chr5:17075800-17081400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr5:17076800-17079800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:17076800-17079800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr5:17076800-17079800	Weak transcription	Fetal Kidney	kidney
8	chr5:17077400-17078400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr5:17077400-17078400	Enhancers	Stomach Mucosa	stomach
10	chr5:17077400-17078400	Enhancers	NHDF-Ad	bronchial
11	chr5:17077600-17078400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:17077600-17078400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr5:17077600-17078400	Enhancers	Adipose Nuclei	Adipose
14	chr5:17077800-17079600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr5:17078000-17078400	Enhancers	NHLF	lung
16	chr5:17078200-17078400	Enhancers	Left Ventricle	heart
17	chr5:17078200-17078800	Enhancers	Placenta	Placenta
18	chr5:17078200-17079600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:17078200-17079800	Weak transcription	Ovary	ovary

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