Variant report

Variant	rs497378
Chromosome Location	chr19:39536375-39536376
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39521423..39523663-chr19:39535001..39537936,2	MCF-7	breast:
2	chr19:39528736..39531074-chr19:39534796..39537090,2	K562	blood:
3	chr19:39521025..39525658-chr19:39535006..39538345,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267992	Chromatin interaction
ENSG00000161243	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10403886	0.86[EUR][1000 genomes]
rs10410965	0.90[CHB][hapmap]
rs1268240	0.90[CHB][hapmap];0.83[JPT][hapmap]
rs1268251	0.84[ASN][1000 genomes]
rs2318896	0.90[CHB][hapmap]
rs2873836	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs472104	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]
rs473729	0.84[ASN][1000 genomes]
rs473878	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]
rs476616	0.91[AMR][1000 genomes];0.99[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	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs485226	0.83[ASN][1000 genomes]
rs533573	0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs536244	0.90[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs569337	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs580494	0.83[ASN][1000 genomes]
rs586059	0.83[ASN][1000 genomes]
rs599752	0.82[EUR][1000 genomes]
rs600128	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs601966	0.90[CHB][hapmap];0.83[JPT][hapmap];0.92[ASN][1000 genomes]
rs603268	0.92[ASN][1000 genomes]
rs617085	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs631879	0.91[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	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7247817	0.91[CHB][hapmap]
rs7254745	0.86[ASN][1000 genomes]
rs7258182	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs8109914	0.90[CHB][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs497378	FBXO27	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39530800-39543000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr19:39535400-39538800	Enhancers	Fetal Intestine Large	intestine
3	chr19:39535400-39538800	Enhancers	Fetal Intestine Small	intestine
4	chr19:39535800-39538800	Enhancers	Duodenum Mucosa	Duodenum
5	chr19:39536200-39536400	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr19:39536200-39536400	Active TSS	HepG2	liver
7	chr19:39536200-39536400	Enhancers	K562	blood
8	chr19:39536200-39536600	Enhancers	A549	lung

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