Variant report

Variant	rs13045415
Chromosome Location	chr20:52410134-52410135
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:40556398..40559378-chr20:52409159..52411423,3	MCF-7	breast:
2	chr20:52407736..52410525-chr7:108165406..108166924,2	MCF-7	breast:
3	chr17:40556379..40559378-chr20:52408311..52410419,2	MCF-7	breast:
4	chr20:52409863..52410427-chr20:55821112..55822035,2	MCF-7	breast:
5	chr20:52410092..52412954-chr20:55842045..55843875,2	MCF-7	breast:
6	chr20:52407579..52410186-chr5:90512301..90513847,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135241	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11086439	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11086440	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4811466	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6022750	0.84[ASN][1000 genomes]
rs6123313	0.81[AMR][1000 genomes]
rs6126949	0.81[AMR][1000 genomes]
rs6126951	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1057509	chr20:52390002-52431309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv586221	chr20:52392390-52418987	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv965888	chr20:52394959-52410541	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	33 gene(s)	inside rSNPs	diseases
7	nsv1064299	chr20:52395560-52420612	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
8	nsv1063442	chr20:52400519-52428220	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
9	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52404200-52414400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr20:52404200-52415600	Weak transcription	Fetal Intestine Large	intestine
3	chr20:52406400-52410800	Weak transcription	HSMMtube	muscle
4	chr20:52406600-52410600	Weak transcription	HepG2	liver
5	chr20:52406600-52417200	Weak transcription	K562	blood
6	chr20:52406800-52413600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr20:52407000-52411200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:52407600-52411200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr20:52407800-52411000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr20:52407800-52411000	Weak transcription	HSMM	muscle
11	chr20:52407800-52411200	Weak transcription	NHDF-Ad	bronchial
12	chr20:52407800-52411600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr20:52408000-52411000	Weak transcription	Osteobl	bone
14	chr20:52408000-52411200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr20:52408000-52411200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr20:52408000-52411200	Weak transcription	NH-A	brain
17	chr20:52408000-52411400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr20:52408000-52413600	Weak transcription	A549	lung
19	chr20:52408200-52410800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr20:52408200-52411200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr20:52408800-52411800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr20:52409200-52411600	Enhancers	NHEK	skin
23	chr20:52409400-52411400	Enhancers	Placenta Amnion	Placenta Amnion
24	chr20:52409400-52411600	Enhancers	Esophagus	oesophagus
25	chr20:52409400-52412200	Enhancers	Placenta	Placenta
26	chr20:52409400-52412600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr20:52409600-52410400	Enhancers	Pancreas	Pancrea
28	chr20:52409600-52411600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr20:52409600-52412000	Enhancers	HMEC	breast
30	chr20:52409600-52412200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr20:52409800-52411200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr20:52410000-52410600	Enhancers	Liver	Liver

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