Variant report

Variant	rs55959219
Chromosome Location	chr5:100248258-100248259
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	chr5:100237355..100239867-chr5:100247037..100249581,2	MCF-7	breast:
2	chr5:100240183..100242753-chr5:100246346..100248554,2	K562	blood:

Variant related genes	Relation type
ENSG00000113532	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs10043056	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10044903	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10052474	0.93[EUR][1000 genomes]
rs10057237	0.84[EUR][1000 genomes]
rs10058901	0.83[EUR][1000 genomes]
rs10059470	0.86[EUR][1000 genomes]
rs10059846	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10069305	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10075853	0.84[EUR][1000 genomes]
rs10078251	0.83[EUR][1000 genomes]
rs10078934	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10214216	0.87[EUR][1000 genomes]
rs10463771	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10463772	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10477661	0.81[EUR][1000 genomes]
rs10478598	0.84[EUR][1000 genomes]
rs10478599	0.84[EUR][1000 genomes]
rs10478633	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10478649	0.81[EUR][1000 genomes]
rs10515303	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11241752	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11241755	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11241794	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11738152	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11741369	0.84[EUR][1000 genomes]
rs11742480	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11742504	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11748306	0.82[EUR][1000 genomes]
rs12153670	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12332145	0.84[EUR][1000 genomes]
rs12332642	0.84[EUR][1000 genomes]
rs12719316	0.85[EUR][1000 genomes]
rs13355889	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13357545	0.84[EUR][1000 genomes]
rs13358325	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13436424	0.84[EUR][1000 genomes]
rs13857	0.84[EUR][1000 genomes]
rs1423380	0.83[EUR][1000 genomes]
rs1423384	0.93[EUR][1000 genomes]
rs1423385	0.93[EUR][1000 genomes]
rs1428439	0.87[EUR][1000 genomes]
rs1541676	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1559058	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1559059	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17723545	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17724185	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17725452	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17725678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17726346	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17780091	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17780273	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17780471	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17780525	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17782041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17782250	0.87[EUR][1000 genomes]
rs1820150	0.81[EUR][1000 genomes]
rs1833862	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059845	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2059846	0.90[EUR][1000 genomes]
rs2400313	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2548257	0.89[EUR][1000 genomes]
rs2548263	0.85[EUR][1000 genomes]
rs2548276	0.81[EUR][1000 genomes]
rs2548278	0.81[EUR][1000 genomes]
rs2548279	0.90[EUR][1000 genomes]
rs2725116	0.81[EUR][1000 genomes]
rs28413976	0.93[EUR][1000 genomes]
rs34564041	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3756350	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3756351	0.87[EUR][1000 genomes]
rs3756352	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3756353	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3756354	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3756355	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3776155	0.84[EUR][1000 genomes]
rs3776167	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3776168	0.91[EUR][1000 genomes]
rs3776170	0.83[EUR][1000 genomes]
rs3776171	0.86[EUR][1000 genomes]
rs3776174	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3776176	0.83[EUR][1000 genomes]
rs3822366	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3843478	0.84[EUR][1000 genomes]
rs3846627	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3857365	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3909452	0.81[EUR][1000 genomes]
rs3909453	0.84[EUR][1000 genomes]
rs4702991	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4703126	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4703127	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4703128	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703130	0.93[EUR][1000 genomes]
rs4703131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55805984	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55849330	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55861847	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55968003	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56752243	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59030588	0.83[EUR][1000 genomes]
rs59490571	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60663279	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60853907	0.84[EUR][1000 genomes]
rs726971	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72776700	0.85[EUR][1000 genomes]
rs72778607	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72778613	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72778620	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72778635	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72778649	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72778650	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7447673	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7703643	0.82[EUR][1000 genomes]
rs7737721	0.81[EUR][1000 genomes]
rs9327319	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9327323	0.94[EUR][1000 genomes]
rs9327327	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs966257	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023765	chr5:99915011-100733755	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	esv1834675	chr5:100143084-100535029	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv882471	chr5:100234439-100362071	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv882472	chr5:100234439-100512338	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv462320	chr5:100247554-100775607	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv599176	chr5:100247554-100775607	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55959219	ST8SIA4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:100246200-100252200	Weak transcription	Dnd41	blood

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