Variant report

Variant	rs17465519
Chromosome Location	chr12:40583821-40583822
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	12:40583667-40584606..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10506145	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564133	0.85[AFR][1000 genomes]
rs11564137	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11564160	0.85[AFR][1000 genomes]
rs11564194	0.86[ASN][1000 genomes]
rs11564276	0.86[ASN][1000 genomes]
rs1482282	0.85[AFR][1000 genomes]
rs1491926	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442108	0.85[AFR][1000 genomes]
rs17442304	0.85[AFR][1000 genomes]
rs17442742	0.86[ASN][1000 genomes]
rs17442749	0.86[ASN][1000 genomes]
rs17442756	0.86[ASN][1000 genomes]
rs17442805	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17442853	0.86[ASN][1000 genomes]
rs17443112	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17443345	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17458299	0.85[AFR][1000 genomes]
rs17458396	0.85[AFR][1000 genomes]
rs17458403	0.85[AFR][1000 genomes]
rs17458752	0.86[ASN][1000 genomes]
rs17458759	0.86[ASN][1000 genomes]
rs17458766	0.86[ASN][1000 genomes]
rs17461492	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17465400	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17465540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17483628	0.84[AFR][1000 genomes]
rs1873610	0.86[ASN][1000 genomes]
rs2046929	0.92[AFR][1000 genomes]
rs2086598	0.85[AFR][1000 genomes]
rs2404574	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708404	1.00[ASN][1000 genomes]
rs28370654	0.85[AFR][1000 genomes]
rs28370656	0.85[AFR][1000 genomes]
rs28370659	0.85[AFR][1000 genomes]
rs28370681	0.85[AFR][1000 genomes]
rs55707305	0.85[AFR][1000 genomes]
rs55993200	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs726330	0.86[ASN][1000 genomes]
rs7305377	0.92[AFR][1000 genomes]
rs7306099	0.86[ASN][1000 genomes]
rs7306718	0.86[ASN][1000 genomes]
rs7308399	0.86[ASN][1000 genomes]
rs7969495	0.85[AFR][1000 genomes]
rs7974522	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974972	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
3	nsv1044685	chr12:40574460-40771612	Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40582200-40584800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr12:40583800-40584400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell

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