Variant report

Variant	rs12590440
Chromosome Location	chr14:66488193-66488194
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:66469138..66471712-chr14:66485442..66488243,2	MCF-7	breast:
2	chr14:66487758..66489942-chr14:66489951..66492637,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258847	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10134858	0.94[ASN][1000 genomes]
rs10142278	1.00[ASN][1000 genomes]
rs10147364	0.94[ASN][1000 genomes]
rs10148230	1.00[ASN][1000 genomes]
rs10498523	1.00[ASN][1000 genomes]
rs12586140	1.00[ASN][1000 genomes]
rs12588471	1.00[ASN][1000 genomes]
rs12588472	1.00[ASN][1000 genomes]
rs12588493	1.00[ASN][1000 genomes]
rs12588504	1.00[ASN][1000 genomes]
rs12588689	1.00[ASN][1000 genomes]
rs12589766	1.00[ASN][1000 genomes]
rs12589905	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12589911	1.00[ASN][1000 genomes]
rs1273869	0.88[ASN][1000 genomes]
rs1273870	1.00[ASN][1000 genomes]
rs1290796	0.86[ASN][1000 genomes]
rs13379051	0.94[ASN][1000 genomes]
rs4258536	1.00[ASN][1000 genomes]
rs4362327	1.00[ASN][1000 genomes]
rs4489934	1.00[ASN][1000 genomes]
rs4540993	1.00[ASN][1000 genomes]
rs4640111	1.00[ASN][1000 genomes]
rs4899191	1.00[ASN][1000 genomes]
rs4899192	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899193	1.00[ASN][1000 genomes]
rs4899194	1.00[ASN][1000 genomes]
rs4902443	0.94[ASN][1000 genomes]
rs4902444	0.94[ASN][1000 genomes]
rs4902445	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4902446	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56231619	0.94[ASN][1000 genomes]
rs56314928	0.94[ASN][1000 genomes]
rs56892961	1.00[ASN][1000 genomes]
rs57146489	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57274818	0.94[ASN][1000 genomes]
rs58000930	1.00[ASN][1000 genomes]
rs59229824	1.00[ASN][1000 genomes]
rs60238746	1.00[ASN][1000 genomes]
rs61085292	1.00[ASN][1000 genomes]
rs73278296	1.00[ASN][1000 genomes]
rs73280006	1.00[ASN][1000 genomes]
rs73280007	1.00[ASN][1000 genomes]
rs768973	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
2	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
3	nsv817409	chr14:66220075-66990168	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv564953	chr14:66287921-67046960	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv1050485	chr14:66308283-67109270	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv530775	chr14:66316836-67079049	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
7	nsv530793	chr14:66317036-67078908	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1046455	chr14:66345369-66848234	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
9	nsv1043864	chr14:66372458-66845503	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
10	nsv917338	chr14:66376591-66841403	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	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
rs12590440	TRAP1	trans	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:66487600-66489200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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