Variant report

Variant	rs3131021
Chromosome Location	chr6:29476142-29476143
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1002187	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1362075	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1592412	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3094564	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3094572	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3128844	0.81[EUR][1000 genomes]
rs3130849	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3130852	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3130854	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3131019	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3131020	0.82[AFR][1000 genomes]
rs734959	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[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	esv3424039	chr6:29439297-29504564	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv883528	chr6:29447724-29494897	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv883529	chr6:29464365-29494897	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3131021	HMGN4	cis	parietal	SCAN
rs3131021	ZKSCAN3	cis	cerebellum	SCAN
rs3131021	C6orf227	cis	parietal	SCAN
rs3131021	SLC17A3	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29468600-29496200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:29475200-29477800	Enhancers	GM12878-XiMat	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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