Variant report

Variant	rs13024519
Chromosome Location	chr2:172452113-172452114
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	chr2:172450683..172452462-chr2:172537710..172539428,2	K562	blood:
2	chr2:172443186..172445133-chr2:172451664..172453720,2	K562	blood:

Variant related genes	Relation type
ENSG00000233934	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10185715	0.81[ASN][1000 genomes]
rs10211146	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10221787	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10432471	0.85[ASN][1000 genomes]
rs10432473	0.80[ASN][1000 genomes]
rs10930485	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11680862	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11680897	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11683752	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11683762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11686621	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11689452	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11689637	0.94[CEU][hapmap];0.82[CHB][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12472229	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12476299	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12996145	0.94[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13002792	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13025303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1807872	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1996268	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2884028	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4667691	0.96[ASN][1000 genomes]
rs4668391	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4668392	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4668393	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4668394	0.94[CHB][hapmap];0.84[JPT][hapmap]
rs6433301	0.80[ASN][1000 genomes]
rs6704691	0.86[ASN][1000 genomes]
rs6711201	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6723896	0.80[ASN][1000 genomes]
rs6745725	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs6747775	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9287946	0.88[JPT][hapmap]
rs9678221	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv997638	chr2:172442205-172560406	Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172451800-172452800	Enhancers	HMEC	breast
2	chr2:172451800-172453000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr2:172451800-172453000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:172451800-172453000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:172451800-172453000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:172451800-172453200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:172451800-172453200	Enhancers	NHDF-Ad	bronchial
8	chr2:172451800-172453200	Enhancers	NHEK	skin
9	chr2:172452000-172452400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr2:172452000-172452400	Enhancers	Adipose Nuclei	Adipose
11	chr2:172452000-172452400	Enhancers	HUVEC	blood vessel
12	chr2:172452000-172452800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:172452000-172452800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:172452000-172452800	Enhancers	Esophagus	oesophagus
15	chr2:172452000-172452800	Enhancers	HSMM	muscle
16	chr2:172452000-172452800	Enhancers	HSMMtube	muscle
17	chr2:172452000-172452800	Flanking Active TSS	Osteobl	bone
18	chr2:172452000-172453000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr2:172452000-172453000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr2:172452000-172453000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:172452000-172453000	Enhancers	A549	lung
22	chr2:172452000-172453000	Enhancers	Hela-S3	cervix
23	chr2:172452000-172453000	Enhancers	NH-A	brain
24	chr2:172452000-172453000	Enhancers	NHLF	lung
25	chr2:172452000-172453200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links