Variant report

Variant	rs10876943
Chromosome Location	chr12:57274648-57274649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10876941	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11172025	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11172033	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17445108	1.00[YRI][hapmap]
rs1846398	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1909328	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2888106	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2888107	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2888108	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4254104	0.91[EUR][1000 genomes]
rs4472974	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4477473	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4759036	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4759041	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4759272	1.00[YRI][hapmap]
rs55812315	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56023460	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61939604	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7303219	0.82[CHB][hapmap];0.81[GIH][hapmap];0.85[MKK][hapmap]
rs7305700	0.88[EUR][1000 genomes]
rs7306442	0.88[CHB][hapmap]
rs7314652	0.87[EUR][1000 genomes]
rs7955918	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956391	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7959253	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7959654	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959725	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7960137	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960618	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7961602	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7967940	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972591	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979655	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840161	0.84[ASW][hapmap];0.89[CEU][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs9668259	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040850	chr12:57055011-57679209	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10876943	RAB5B	cis	parietal	SCAN
rs10876943	BIN2	cis	cerebellum	SCAN
rs10876943	APOF	cis	parietal	SCAN
rs10876943	GALNT6	cis	parietal	SCAN
rs10876943	RDH16	cis	cerebellum	SCAN
rs10876943	ACVR1B	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57273400-57275000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr12:57274000-57274800	Enhancers	Osteobl	bone
3	chr12:57274000-57275000	Enhancers	A549	lung
4	chr12:57274000-57275200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:57274000-57275200	Enhancers	HSMMtube	muscle
6	chr12:57274000-57275400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:57274000-57275400	Enhancers	HSMM	muscle
8	chr12:57274000-57275600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:57274000-57275600	Enhancers	K562	blood
10	chr12:57274200-57274800	Enhancers	Primary T cells from cord blood	blood
11	chr12:57274200-57274800	Enhancers	Fetal Kidney	kidney
12	chr12:57274200-57275000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:57274200-57275800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:57274400-57275400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr12:57274600-57275000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:57274600-57280000	Weak transcription	Liver	Liver

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