Variant report

Variant	rs449242
Chromosome Location	chr6:33496714-33496715
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33385003..33387538-chr6:33494085..33496852,2	K562	blood:
2	chr6:33265668..33268001-chr6:33494684..33497652,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112514	Chromatin interaction
ENSG00000237441	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11757081	0.85[CHB][hapmap]
rs1794687	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs191902	0.89[EUR][1000 genomes]
rs210134	0.86[YRI][hapmap]
rs210177	0.89[EUR][1000 genomes]
rs210178	0.88[EUR][1000 genomes]
rs210180	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs210182	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs210183	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs210184	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs210185	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs210186	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs210187	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs210192	0.93[EUR][1000 genomes]
rs210196	0.96[CEU][hapmap];0.86[GIH][hapmap];0.83[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs210197	0.96[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs210202	0.80[CEU][hapmap]
rs210203	0.84[CEU][hapmap];0.82[GIH][hapmap]
rs210207	0.84[CEU][hapmap]
rs210209	0.82[CEU][hapmap]
rs367408	1.00[CEU][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs367897	1.00[CEU][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs368429	0.86[EUR][1000 genomes]
rs368716	1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs371155	1.00[CEU][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs372469	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs372846	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs380163	1.00[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs383936	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs386879	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3916269	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs396516	1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs404778	1.00[CEU][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs405126	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs447418	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73404347	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9461874	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9469481	1.00[CEU][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9469483	1.00[CEU][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv524010	chr6:33468151-33505981	Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	esv2763548	chr6:33496201-33524779	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs449242	FTSJD2	cis	cerebellum	SCAN
rs449242	CDKN1A	cis	parietal	SCAN
rs449242	HLA-DRB5	cis	parietal	SCAN
rs449242	UHRF1BP1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33494600-33497400	Weak transcription	HepG2	liver
2	chr6:33496200-33496800	Enhancers	Fetal Stomach	stomach
3	chr6:33496400-33496800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr6:33496400-33496800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:33496400-33496800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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