Variant report

Variant	rs6540571
Chromosome Location	chr1:210123882-210123883
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1016479	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1099864	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17188183	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17188190	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2142857	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2205990	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2235371	1.00[LWK][hapmap]
rs227185	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs227192	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs227208	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs227214	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs227215	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2357211	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2451693	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2484029	0.90[AMR][1000 genomes]
rs2494187	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2494188	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2743892	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61820363	0.81[EUR][1000 genomes]
rs61820393	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61827913	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs719034	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72741075	0.85[EUR][1000 genomes]
rs846547	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs923561	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873140	chr1:210068117-210335644	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1825811	chr1:210082206-210135806	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv1821002	chr1:210108473-210291476	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6540571	MAFB	trans	lymphoblastoid	seeQTL
rs6540571	G0S2	cis	lymphoblastoid	seeQTL
rs6540571	IKBKE	cis	parietal	SCAN
rs6540571	CR1L	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210112600-210128400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:210120000-210136000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:210120800-210126400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:210123800-210124000	Enhancers	Brain Cingulate Gyrus	brain

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