Variant report

Variant	rs2493224
Chromosome Location	chr6:79080410-79080411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10455116	0.89[ASN][1000 genomes]
rs12199172	0.83[ASN][1000 genomes]
rs12215169	0.83[ASN][1000 genomes]
rs13214425	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1349662	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1452529	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1452530	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1452531	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1452533	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs145675	0.97[ASN][1000 genomes]
rs1584756	0.89[EUR][1000 genomes]
rs1597835	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171027	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1901613	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2123307	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2206831	0.83[ASN][1000 genomes]
rs2206832	0.89[ASN][1000 genomes]
rs2223722	0.83[ASN][1000 genomes]
rs2262380	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262381	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs235452	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235453	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs235454	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235455	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs235456	0.97[ASN][1000 genomes]
rs235457	0.88[EUR][1000 genomes]
rs236247	0.96[ASN][1000 genomes]
rs236254	0.97[ASN][1000 genomes]
rs236255	0.98[ASN][1000 genomes]
rs236258	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs236259	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2444196	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2444197	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444202	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2493225	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2493226	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493228	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493229	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493233	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2493237	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392084	0.88[EUR][1000 genomes]
rs4706703	0.89[ASN][1000 genomes]
rs56047396	0.89[ASN][1000 genomes]
rs62426486	0.94[ASN][1000 genomes]
rs62426487	0.94[ASN][1000 genomes]
rs7752809	0.83[ASN][1000 genomes]
rs926654	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758064	chr6:78795880-79193468	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
2	esv2759447	chr6:78795880-79193468	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv886235	chr6:78861808-79369972	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv428149	chr6:78890476-79099763	Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2757181	chr6:78944539-79094007	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv821650	chr6:79002204-79095287	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1018006	chr6:79003806-79228498	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv604011	chr6:79042990-79455282	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv7931	chr6:79078579-79080460	Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2493224	HMGN3	cis	parietal	SCAN
rs2493224	BCKDHB	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79080200-79080800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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