Variant report

Variant	rs2113420
Chromosome Location	chr2:53463136-53463137
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs13421013	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1364662	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1364663	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1559631	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs171877	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1834277	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1863178	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863179	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1863180	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs195572	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs195573	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs195574	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs195576	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs195577	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs195581	0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs195588	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs195589	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs195590	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs195591	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs195592	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs195593	0.85[ASN][1000 genomes]
rs7562698	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7574564	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs933786	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs933788	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751897	chr2:53358205-53475338	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1002145	chr2:53387912-53832213	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv535718	chr2:53387912-53832213	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2113420	CHAC2	cis	parietal	SCAN
rs2113420	ACYP2	cis	parietal	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53456600-53464000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr2:53459600-53464200	Enhancers	Dnd41	blood
3	chr2:53461200-53463200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:53461400-53464000	Enhancers	Primary hematopoietic stem cells	blood
5	chr2:53461400-53464200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr2:53461600-53463600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:53461600-53463800	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr2:53461800-53463200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:53462000-53463600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:53462000-53464200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:53462600-53463200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:53462600-53463600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:53462600-53463800	Enhancers	HUVEC	blood vessel
14	chr2:53462800-53463400	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr2:53463000-53463200	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr2:53463000-53463200	Enhancers	Fetal Thymus	thymus
17	chr2:53463000-53463400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:53463000-53463400	Enhancers	NHEK	skin
19	chr2:53463000-53463600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:53463000-53463600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:53463000-53463600	Enhancers	Colonic Mucosa	Colon
22	chr2:53463000-53463600	Enhancers	Fetal Kidney	kidney

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