Variant report

Variant	rs12496235
Chromosome Location	chr3:160885975-160885976
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160815777..160819768-chr3:160885068..160889447,5	MCF-7	breast:
2	chr3:160876047..160878704-chr3:160883637..160886578,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1017799	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10513561	0.90[JPT][hapmap]
rs10513562	0.81[JPT][hapmap]
rs12485519	0.84[ASN][1000 genomes]
rs12486069	1.00[ASN][1000 genomes]
rs12486103	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12487156	0.90[JPT][hapmap]
rs12489004	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12489125	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12490149	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12493266	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12494725	0.84[AMR][1000 genomes]
rs12496837	0.81[AMR][1000 genomes]
rs13315320	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13319558	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13319771	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16831799	1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16831850	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16831864	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16831882	1.00[ASN][1000 genomes]
rs16831942	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2306209	0.85[AMR][1000 genomes]
rs28451189	0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28704960	1.00[ASN][1000 genomes]
rs28713364	0.94[AMR][1000 genomes]
rs3925722	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4296611	0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4352387	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4468992	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4580574	0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4635725	0.97[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56807417	0.82[AMR][1000 genomes]
rs57903480	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59567999	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59593286	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59757775	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs59776766	1.00[ASN][1000 genomes]
rs59867530	0.84[AMR][1000 genomes]
rs60121330	1.00[ASN][1000 genomes]
rs6441350	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6441363	0.97[AMR][1000 genomes]
rs6441365	0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6441372	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6441375	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6762064	0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6771581	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6774919	0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6775446	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6775931	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6778186	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6782415	0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6782518	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6785714	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6787447	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6788738	0.94[AMR][1000 genomes]
rs6790705	0.82[CHB][hapmap];0.81[JPT][hapmap];0.82[AMR][1000 genomes]
rs6790805	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6796168	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6801664	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6805976	0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6806054	0.81[JPT][hapmap]
rs73017340	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73019384	0.82[AMR][1000 genomes]
rs73026933	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs73026967	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73026968	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73026983	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73026987	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73026989	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs734915	0.84[ASN][1000 genomes]
rs73878309	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7615833	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7615868	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7624791	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7626773	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7627500	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7632423	0.80[JPT][hapmap]
rs7634299	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7639529	0.82[AMR][1000 genomes]
rs7651924	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7652624	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs778653	0.80[JPT][hapmap]
rs9290070	0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9290071	0.97[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9682249	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9682995	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9810351	1.00[ASN][1000 genomes]
rs9812574	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9818470	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9818835	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9818992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9819793	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9822705	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9822916	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9823424	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824535	1.00[ASN][1000 genomes]
rs9824805	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9826857	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9830183	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9833270	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9834806	0.97[AMR][1000 genomes]
rs9835530	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9838945	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9841871	0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9842290	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9847842	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9851699	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9855112	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9855572	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9856742	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9858907	1.00[ASN][1000 genomes]
rs9859641	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9860980	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9862867	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9871753	0.94[YRI][hapmap];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9875200	0.81[JPT][hapmap]
rs9876077	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9877309	0.97[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9880536	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9884100	0.97[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9985364	0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160881000-160886400	Weak transcription	Fetal Heart	heart
2	chr3:160883200-160888600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:160883200-160889000	Weak transcription	Ovary	ovary

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