Variant report

Variant	rs472104
Chromosome Location	chr19:39533937-39533938
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	chr19:39519101..39521598-chr19:39532998..39534703,2	K562	blood:

Variant related genes	Relation type
ENSG00000267992	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 5 )

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	0.84[ASN][1000 genomes]
rs2318896	0.90[CHB][hapmap];0.95[CHD][hapmap]
rs2873836	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs473729	0.84[ASN][1000 genomes]
rs473878	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]
rs476616	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479001	0.84[ASN][1000 genomes]
rs4802004	0.85[ASN][1000 genomes]
rs4802012	0.90[ASN][1000 genomes]
rs4803194	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs485226	0.83[ASN][1000 genomes]
rs497378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533573	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs536244	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs569337	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs580494	0.83[ASN][1000 genomes]
rs586059	0.83[ASN][1000 genomes]
rs599752	0.81[EUR][1000 genomes]
rs600128	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs601966	0.90[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs603268	0.92[ASN][1000 genomes]
rs617085	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs631879	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs631952	0.84[ASN][1000 genomes]
rs646580	0.83[ASN][1000 genomes]
rs650450	0.92[ASN][1000 genomes]
rs681921	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7247817	0.90[CHB][hapmap]
rs7254745	0.86[ASN][1000 genomes]
rs7258182	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs8109914	0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs472104	PTGIR	cis	parietal	SCAN
rs472104	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx
rs472104	FBXO27	cis	lymphoblastoid	seeQTL
rs472104	ZNF45	cis	parietal	SCAN
rs472104	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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