Variant report

Variant	rs2409556
Chromosome Location	chr13:55407639-55407640
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11839135	0.84[EUR][1000 genomes]
rs12184758	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1462189	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1531450	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1531451	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1551834	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1599559	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs2000176	0.86[AFR][1000 genomes]
rs2409555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4460957	0.85[AFR][1000 genomes]
rs55774097	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59443607	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6561803	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6561804	0.84[EUR][1000 genomes]
rs6561805	0.84[EUR][1000 genomes]
rs7317573	0.84[EUR][1000 genomes]
rs7320026	0.84[EUR][1000 genomes]
rs73202867	0.87[EUR][1000 genomes]
rs73202894	0.86[EUR][1000 genomes]
rs73204603	0.84[EUR][1000 genomes]
rs73204607	0.84[EUR][1000 genomes]
rs73204610	0.84[EUR][1000 genomes]
rs73204611	0.84[EUR][1000 genomes]
rs73204613	0.82[EUR][1000 genomes]
rs73204615	0.84[EUR][1000 genomes]
rs73204619	0.84[EUR][1000 genomes]
rs73204620	0.84[EUR][1000 genomes]
rs73204623	0.84[EUR][1000 genomes]
rs73204626	0.84[EUR][1000 genomes]
rs73204627	0.84[EUR][1000 genomes]
rs73204633	0.84[EUR][1000 genomes]
rs7321772	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7989867	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7991935	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9527289	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9536881	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9536893	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9597053	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9805429	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][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	nsv917186	chr13:55022134-55433232	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv561702	chr13:55086271-55808127	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1048599	chr13:55143426-55476042	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1051640	chr13:55143426-55478547	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv561703	chr13:55143754-55473732	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv916104	chr13:55154006-55433232	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1052745	chr13:55159674-55459161	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv541779	chr13:55159674-55459161	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv900096	chr13:55363417-55508485	Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv561704	chr13:55395253-55764633	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 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	chr13:55404000-55408400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr13:55407600-55408200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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