Variant report

Variant	rs6782079
Chromosome Location	chr3:23626919-23626920
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11914576	0.82[EUR][1000 genomes]
rs11919065	0.82[EUR][1000 genomes]
rs11926217	0.85[EUR][1000 genomes]
rs11926646	0.94[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12486880	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12637722	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1463836	1.00[CEU][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17013457	0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1874913	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2133330	0.88[GIH][hapmap];0.84[TSI][hapmap]
rs35169377	0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4399836	0.95[ASN][1000 genomes]
rs55666330	0.87[EUR][1000 genomes]
rs55732421	0.87[EUR][1000 genomes]
rs55779138	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56132801	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56667039	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57989144	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59580282	0.82[EUR][1000 genomes]
rs60221455	0.87[EUR][1000 genomes]
rs60759404	0.82[EUR][1000 genomes]
rs61363919	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6550765	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66900833	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6775891	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6775907	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778020	0.97[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6799118	0.85[EUR][1000 genomes]
rs6799234	0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs6800822	0.93[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6801946	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6802488	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804201	1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs73045660	0.87[EUR][1000 genomes]
rs73049414	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7609845	0.88[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7610906	0.81[GIH][hapmap]
rs7624174	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628135	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7628949	0.93[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7631705	0.85[EUR][1000 genomes]
rs7640458	0.88[GIH][hapmap];0.82[TSI][hapmap]
rs9812300	0.88[GIH][hapmap];0.82[TSI][hapmap]
rs9854488	0.95[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs9873979	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[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	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv460479	chr3:23626919-23807550	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv589949	chr3:23626919-23807550	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6782079	KAT2B	cis	parietal	SCAN
rs6782079	SLC4A7	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23606000-23643000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:23607000-23640400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:23608600-23634400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr3:23609400-23637800	Weak transcription	HSMMtube	muscle
5	chr3:23617200-23635600	Weak transcription	Fetal Thymus	thymus
6	chr3:23620400-23629200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:23621000-23642800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:23622400-23637800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:23623800-23632200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr3:23623800-23634400	Weak transcription	Primary B cells from cord blood	blood
11	chr3:23624400-23641600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr3:23624800-23630400	Weak transcription	Right Atrium	heart
13	chr3:23625400-23637800	Weak transcription	H9 Cell Line	embryonic stem cell

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