Variant report

Variant	rs56267813
Chromosome Location	chr1:76248707-76248708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1061337	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10873685	0.84[EUR][1000 genomes]
rs11161437	0.85[EUR][1000 genomes]
rs11161468	0.82[EUR][1000 genomes]
rs11161510	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11161511	0.84[EUR][1000 genomes]
rs11161515	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11161521	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11161620	0.82[EUR][1000 genomes]
rs11161626	0.82[EUR][1000 genomes]
rs1144336	0.80[EUR][1000 genomes]
rs1146653	0.80[EUR][1000 genomes]
rs12091720	0.83[EUR][1000 genomes]
rs12093623	0.82[EUR][1000 genomes]
rs12094842	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12122939	0.81[EUR][1000 genomes]
rs12123977	0.84[EUR][1000 genomes]
rs12126481	0.80[EUR][1000 genomes]
rs12126607	0.84[EUR][1000 genomes]
rs12127078	0.82[EUR][1000 genomes]
rs12127402	0.84[EUR][1000 genomes]
rs1498312	0.82[EUR][1000 genomes]
rs1498316	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17587071	0.85[EUR][1000 genomes]
rs1855136	0.81[EUR][1000 genomes]
rs1890451	0.84[EUR][1000 genomes]
rs2185152	0.84[EUR][1000 genomes]
rs2211080	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28602663	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4559448	0.84[EUR][1000 genomes]
rs4646961	0.84[EUR][1000 genomes]
rs4949674	0.84[EUR][1000 genomes]
rs4949677	0.82[EUR][1000 genomes]
rs4949875	0.82[EUR][1000 genomes]
rs4949876	0.81[EUR][1000 genomes]
rs4949877	0.84[EUR][1000 genomes]
rs4949879	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56352044	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5745336	0.82[EUR][1000 genomes]
rs5745363	0.81[EUR][1000 genomes]
rs61289992	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61622554	0.85[EUR][1000 genomes]
rs61797339	0.83[EUR][1000 genomes]
rs61797340	0.86[EUR][1000 genomes]
rs61799967	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61799988	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61799990	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72686191	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7513559	0.83[EUR][1000 genomes]
rs7516226	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524467	0.84[EUR][1000 genomes]
rs7534754	0.83[EUR][1000 genomes]
rs7539246	0.84[EUR][1000 genomes]
rs7547056	0.81[EUR][1000 genomes]
rs942270	0.84[EUR][1000 genomes]
rs9662166	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[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	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830281	chr1:76095292-76251053	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1014072	chr1:76200531-76460726	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv535005	chr1:76200531-76460726	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs56267813	RABGGTB	Cis_1M	lymphoblastoid	RTeQTL
rs56267813	ACADM	cis	Whole Blood	GTEx
rs56267813	ACADM	cis	Muscle Skeletal	GTEx

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76227400-76249800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:76241400-76251000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:76241400-76251200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr1:76244400-76250800	Weak transcription	HepG2	liver

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