Variant report

Variant	rs13424253
Chromosome Location	chr2:46616065-46616066
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:46300290..46302585-chr2:46613885..46616357,2	MCF-7	breast:
2	chr2:46609393..46611243-chr2:46614056..46616065,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171132	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11689649	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11689694	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11689989	0.82[AMR][1000 genomes]
rs11690950	0.89[CHB][hapmap]
rs13019414	0.80[ASN][1000 genomes]
rs3088359	0.85[CHB][hapmap];0.81[MEX][hapmap]
rs4450662	0.94[CHD][hapmap];0.82[GIH][hapmap]
rs55864213	0.81[AMR][1000 genomes]
rs56058321	0.81[AMR][1000 genomes]
rs56768253	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7571218	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs7590087	0.85[CHB][hapmap];0.82[ASN][1000 genomes]
rs7605241	0.84[AMR][1000 genomes]
rs7606737	0.94[CHD][hapmap];0.82[GIH][hapmap];0.81[ASN][1000 genomes]
rs9677412	0.81[CEU][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv916169	chr2:46310963-46622603	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
5	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46589800-46616600	Weak transcription	Thymus	Thymus
2	chr2:46592200-46619800	Weak transcription	K562	blood
3	chr2:46592600-46616200	Strong transcription	Placenta Amnion	Placenta Amnion
4	chr2:46601800-46616400	Genic enhancers	Placenta	Placenta
5	chr2:46607000-46617000	Weak transcription	Stomach Mucosa	stomach
6	chr2:46609000-46617000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:46611200-46616800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:46611600-46616600	Weak transcription	Fetal Intestine Large	intestine
9	chr2:46612000-46616800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:46612000-46620600	Weak transcription	Psoas Muscle	Psoas
11	chr2:46612000-46622400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:46612600-46617000	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr2:46612800-46616600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:46613200-46616600	Weak transcription	Ovary	ovary
15	chr2:46613200-46644200	Weak transcription	Aorta	Aorta
16	chr2:46613400-46616200	Weak transcription	Fetal Muscle Leg	muscle
17	chr2:46613400-46616600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:46613400-46616600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:46613400-46616600	Weak transcription	Gastric	stomach
20	chr2:46613400-46616800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr2:46613400-46617200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:46613400-46617400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:46613400-46617400	Weak transcription	Colonic Mucosa	Colon
24	chr2:46613600-46616800	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr2:46614000-46617200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:46614200-46616400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:46614200-46616400	Enhancers	Brain Substantia Nigra	brain
28	chr2:46614200-46616800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr2:46614400-46616200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:46614400-46616200	Enhancers	Right Atrium	heart
31	chr2:46614400-46616400	Enhancers	Brain Angular Gyrus	brain
32	chr2:46614400-46616400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
33	chr2:46614400-46617200	Enhancers	Brain Hippocampus Middle	brain
34	chr2:46614400-46620600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr2:46614600-46616200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr2:46614600-46616400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:46614600-46617600	Enhancers	HepG2	liver
38	chr2:46614600-46623000	Weak transcription	Esophagus	oesophagus
39	chr2:46615200-46616800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr2:46615400-46616200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:46615400-46624800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:46615600-46616800	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr2:46615600-46617200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr2:46615600-46617400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr2:46615600-46620000	Weak transcription	Lung	lung
46	chr2:46615600-46620000	Weak transcription	HUVEC	blood vessel
47	chr2:46615600-46622400	Weak transcription	Spleen	Spleen
48	chr2:46615800-46616200	Enhancers	Left Ventricle	heart
49	chr2:46615800-46616800	Enhancers	Right Ventricle	heart
50	chr2:46615800-46617400	Enhancers	Adipose Nuclei	Adipose

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