Variant report

Variant	rs2024766
Chromosome Location	chr1:184653633-184653634
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1040666	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs1046239	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1061508	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10752941	0.80[EUR][1000 genomes]
rs10797987	0.85[EUR][1000 genomes]
rs10911631	0.81[AMR][1000 genomes]
rs10911644	0.86[CHB][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap]
rs10911645	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12032144	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12043236	0.80[EUR][1000 genomes]
rs12071631	0.92[CEU][hapmap];0.87[GIH][hapmap]
rs12124714	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12124929	1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs12131285	0.86[CHB][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes]
rs12567225	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs12567226	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs2024764	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2024765	0.87[EUR][1000 genomes]
rs2024767	0.92[CEU][hapmap];0.87[GIH][hapmap]
rs2064605	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2207733	0.80[EUR][1000 genomes]
rs2333715	0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs2333716	0.92[CEU][hapmap];0.86[GIH][hapmap]
rs35478695	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3736757	0.92[CEU][hapmap];0.87[GIH][hapmap];0.81[EUR][1000 genomes]
rs3895196	0.81[GIH][hapmap]
rs4469687	0.80[EUR][1000 genomes]
rs4651230	0.86[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap]
rs6663178	0.88[CEU][hapmap];0.85[GIH][hapmap];0.81[EUR][1000 genomes]
rs6677073	0.83[EUR][1000 genomes]
rs726427	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7523023	0.81[EUR][1000 genomes]
rs7525074	0.80[EUR][1000 genomes]
rs861578	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs861581	0.91[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9425338	0.81[AMR][1000 genomes]
rs9425340	0.81[AMR][1000 genomes]
rs9425341	0.81[EUR][1000 genomes]
rs9425343	0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap]
rs9425632	0.81[AMR][1000 genomes]
rs9425633	0.82[EUR][1000 genomes]
rs9425634	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9425635	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9658937	0.82[EUR][1000 genomes]
rs9661314	0.82[EUR][1000 genomes]
rs971080	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9787132	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756618	chr1:184393343-184674343	Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS 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	69 gene(s)	inside rSNPs	diseases
4	nsv832037	chr1:184568194-184756597	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2024766	EDEM3	Cis_1M	lymphoblastoid	RTeQTL
rs2024766	EDEM3	cis	Esophagus Muscularis	GTEx
rs2024766	PRG4	cis	parietal	SCAN
rs2024766	IER5	cis	cerebellum	SCAN
rs2024766	FAM129A	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184641400-184672800	Weak transcription	Gastric	stomach
2	chr1:184649400-184662800	Weak transcription	Osteobl	bone
3	chr1:184652200-184655000	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr1:184652800-184653800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:184653200-184705000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:184653400-184654200	Enhancers	Colon Smooth Muscle	Colon
7	chr1:184653400-184654400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:184653400-184654400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:184653400-184654800	Enhancers	Fetal Lung	lung
10	chr1:184653600-184653800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:184653600-184653800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:184653600-184654600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links