Variant report

Variant	rs473878
Chromosome Location	chr19:39533754-39533755
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39519101..39521598-chr19:39532998..39534703,2	K562	blood:
2	chr19:39527434..39530385-chr19:39532161..39533802,2	K562	blood:

Variant related genes	Relation type
ENSG00000267992	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10403886	0.86[EUR][1000 genomes]
rs10410965	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs1268240	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap]
rs1268251	0.83[ASN][1000 genomes]
rs2318896	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs2873836	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs472104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs473729	0.83[ASN][1000 genomes]
rs476616	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs479001	0.83[ASN][1000 genomes]
rs4802004	0.84[ASN][1000 genomes]
rs4802012	0.89[ASN][1000 genomes]
rs4803194	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs485226	0.81[ASN][1000 genomes]
rs497378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs533573	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.83[ASN][1000 genomes]
rs536244	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs569337	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs580494	0.81[ASN][1000 genomes]
rs586059	0.81[ASN][1000 genomes]
rs599752	0.82[EUR][1000 genomes]
rs600128	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs601966	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];1.00[MKK][hapmap];0.90[ASN][1000 genomes]
rs603268	0.90[ASN][1000 genomes]
rs617085	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs631879	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs631952	0.83[ASN][1000 genomes]
rs646580	0.81[ASN][1000 genomes]
rs650450	0.90[ASN][1000 genomes]
rs681921	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7247817	0.90[CHB][hapmap]
rs7254745	0.84[ASN][1000 genomes]
rs7258182	0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs8109914	0.90[CHB][hapmap];0.95[CHD][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv963126	chr19:39521120-39552490	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv2760517	chr19:39530012-39544234	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv526711	chr19:39533754-39538592	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv458570	chr19:39533754-39538592	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv579507	chr19:39533754-39538592	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv458571	chr19:39533754-39628050	Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv579508	chr19:39533754-39628050	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs473878	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs473878	PTGIR	cis	parietal	SCAN
rs473878	ZNF45	cis	parietal	SCAN
rs473878	ATP5SL	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39523400-39535400	Weak transcription	Right Atrium	heart
2	chr19:39530800-39543000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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