Variant report

Variant	rs236248
Chromosome Location	chr6:79109371-79109372
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10455345	0.92[ASN][1000 genomes]
rs12192598	0.88[ASN][1000 genomes]
rs12194127	0.88[ASN][1000 genomes]
rs12194220	0.88[ASN][1000 genomes]
rs12209135	0.88[ASN][1000 genomes]
rs12213776	0.97[ASN][1000 genomes]
rs13214425	0.85[EUR][1000 genomes]
rs1452529	0.86[EUR][1000 genomes]
rs1452530	0.83[EUR][1000 genomes]
rs1452535	0.97[ASN][1000 genomes]
rs1584756	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1597835	0.85[EUR][1000 genomes]
rs171027	0.87[EUR][1000 genomes]
rs1901613	0.86[EUR][1000 genomes]
rs2123307	0.85[EUR][1000 genomes]
rs2262381	0.88[EUR][1000 genomes]
rs2321307	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs235452	0.82[EUR][1000 genomes]
rs235453	0.81[EUR][1000 genomes]
rs235457	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs236246	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236247	0.81[EUR][1000 genomes]
rs236250	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236251	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236252	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236253	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236254	0.89[EUR][1000 genomes]
rs236255	0.80[EUR][1000 genomes]
rs236259	0.82[EUR][1000 genomes]
rs236260	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs236261	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444196	0.83[EUR][1000 genomes]
rs2444197	0.86[EUR][1000 genomes]
rs2493226	0.83[EUR][1000 genomes]
rs2493233	0.85[EUR][1000 genomes]
rs392084	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs72894264	0.92[ASN][1000 genomes]
rs9448389	0.92[ASN][1000 genomes]
rs9448394	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	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	nsv1018006	chr6:79003806-79228498	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs236248	HMGN3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:79108200-79109400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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