Variant report

Variant	rs28642966
Chromosome Location	chr4:47945295-47945296
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:47942692..47945370-chr4:47945557..47947675,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10002500	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10014206	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10015582	0.92[YRI][hapmap]
rs10028155	0.80[AFR][1000 genomes]
rs10049713	0.90[YRI][hapmap]
rs10517200	0.92[CEU][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs11733288	0.80[CHB][hapmap];0.80[JPT][hapmap]
rs12645164	0.92[CEU][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes]
rs12645245	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs12645873	0.92[EUR][1000 genomes]
rs1371732	0.81[CHB][hapmap]
rs16860680	0.92[YRI][hapmap]
rs17601719	0.92[EUR][1000 genomes]
rs17654502	0.92[EUR][1000 genomes]
rs17654526	0.91[EUR][1000 genomes]
rs1866688	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28392911	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28699496	0.97[EUR][1000 genomes]
rs28806296	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3113881	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs321623	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs321633	0.86[CHB][hapmap];0.83[GIH][hapmap];0.80[JPT][hapmap]
rs3950558	0.91[ASW][hapmap];0.81[CHB][hapmap];0.80[JPT][hapmap];0.80[LWK][hapmap];0.80[MKK][hapmap]
rs55684720	0.92[EUR][1000 genomes]
rs6447603	0.81[CHB][hapmap]
rs6815011	0.92[CEU][hapmap];0.80[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs73814824	0.86[EUR][1000 genomes]
rs9994204	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9998800	0.92[YRI][hapmap]

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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28642966	NFXL1	cis	Whole Blood	GTEx
rs28642966	CNGA1	cis	Muscle Skeletal	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47936400-47950600	Weak transcription	Liver	Liver
2	chr4:47944400-47945400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr4:47945200-47946400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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