Variant report

Variant	rs1102558
Chromosome Location	chr6:27152528-27152529
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27138251..27140956-chr6:27151382..27153649,2	K562	blood:
2	chr6:27145218..27148337-chr6:27151646..27158450,9	MCF-7	breast:
3	chr6:27150672..27153341-chr6:27153761..27155795,3	MCF-7	breast:
4	chr6:27148219..27154668-chr6:27154722..27158254,9	K562	blood:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1102559	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1102560	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1102563	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1102564	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1102565	0.82[ASN][1000 genomes]
rs2393915	0.86[CHB][hapmap]
rs2753120	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4713069	0.90[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs60266855	0.83[EUR][1000 genomes]
rs6456768	0.86[CHB][hapmap]
rs858967	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858970	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858972	0.89[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs858973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs858974	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs858975	0.81[ASN][1000 genomes]
rs858976	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs858980	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs858982	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs911186	0.82[YRI][hapmap]
rs994691	0.86[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1102558	HMGN4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27146600-27155800	Weak transcription	Spleen	Spleen
2	chr6:27146800-27155400	Weak transcription	Adipose Nuclei	Adipose
3	chr6:27147000-27155000	Weak transcription	Right Atrium	heart
4	chr6:27147000-27155600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:27152200-27153400	Weak transcription	K562	blood

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