Variant report

Variant	rs6016716
Chromosome Location	chr20:40830891-40830892
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:40830590..40835735-chr20:55836914..55842550,8	MCF-7	breast:
2	chr20:40829528..40831180-chr3:64091898..64094307,2	MCF-7	breast:
3	chr20:40818651..40823257-chr20:40826391..40832084,7	MCF-7	breast:
4	chr20:40829620..40834300-chr20:55837040..55842828,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000226308	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs1014757	0.84[ASN][1000 genomes]
rs11907691	0.84[ASN][1000 genomes]
rs12625238	0.92[ASN][1000 genomes]
rs13040788	0.93[ASN][1000 genomes]
rs1883376	0.83[ASN][1000 genomes]
rs1883377	0.83[ASN][1000 genomes]
rs1883378	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1984399	0.88[EUR][1000 genomes]
rs2143008	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2143632	0.82[ASN][1000 genomes]
rs2179336	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2206168	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2206169	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2223425	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2223426	0.90[ASN][1000 genomes]
rs2223718	0.92[ASN][1000 genomes]
rs2867061	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2867062	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2867063	0.90[ASN][1000 genomes]
rs2903465	0.90[ASN][1000 genomes]
rs4140521	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4331574	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4425144	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4507153	0.95[EUR][1000 genomes]
rs6016705	0.89[ASN][1000 genomes]
rs6016706	0.85[ASN][1000 genomes]
rs6016707	0.90[ASN][1000 genomes]
rs6016708	0.90[ASN][1000 genomes]
rs6016709	0.90[ASN][1000 genomes]
rs6016710	0.90[ASN][1000 genomes]
rs6016711	0.89[ASN][1000 genomes]
rs6016712	0.89[ASN][1000 genomes]
rs6016713	0.89[ASN][1000 genomes]
rs6016726	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6030023	0.85[ASN][1000 genomes]
rs6030026	0.85[ASN][1000 genomes]
rs6030027	0.89[ASN][1000 genomes]
rs6030029	0.90[ASN][1000 genomes]
rs6030033	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6030035	0.89[ASN][1000 genomes]
rs6030036	0.87[ASN][1000 genomes]
rs6030037	0.89[ASN][1000 genomes]
rs6030056	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6030061	0.85[ASN][1000 genomes]
rs6030069	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6030070	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6030071	0.88[EUR][1000 genomes]
rs6030073	0.84[ASN][1000 genomes]
rs6030076	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6030078	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6030081	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6030082	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6030083	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6030084	0.82[EUR][1000 genomes]
rs6030085	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6030087	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6030088	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6030089	0.88[EUR][1000 genomes]
rs6030096	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6030100	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6030101	0.87[AMR][1000 genomes]
rs6065450	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6065451	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6072651	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6072672	0.87[AMR][1000 genomes]
rs6093584	0.85[ASN][1000 genomes]
rs6093588	0.86[ASN][1000 genomes]
rs6093589	0.89[ASN][1000 genomes]
rs6102704	0.85[ASN][1000 genomes]
rs6102713	0.90[ASN][1000 genomes]
rs6102714	0.86[ASN][1000 genomes]
rs6124427	0.90[ASN][1000 genomes]
rs6124429	0.92[ASN][1000 genomes]
rs6124435	0.88[EUR][1000 genomes]
rs6130071	0.86[ASN][1000 genomes]
rs6130073	0.91[ASN][1000 genomes]
rs6130074	0.91[ASN][1000 genomes]
rs6130076	0.96[ASN][1000 genomes]
rs6130081	0.83[ASN][1000 genomes]
rs6130091	0.87[EUR][1000 genomes]
rs7270492	0.85[ASN][1000 genomes]
rs727336	0.87[EUR][1000 genomes]
rs728373	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs728374	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs742290	0.89[ASN][1000 genomes]
rs742291	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs926647	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs932358	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs979634	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751913	chr20:40422982-41269321	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv532516	chr20:40451059-41097155	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 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	chr20:40828000-40850400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr20:40828600-40833000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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