Variant report

Variant	rs9842290
Chromosome Location	chr3:161000147-161000148
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160998590..161004098-chr3:161031167..161035957,5	MCF-7	breast:
2	chr3:160999120..161000836-chr3:161086906..161089485,3	MCF-7	breast:
3	chr3:160999506..161001764-chr3:161085890..161088412,2	MCF-7	breast:
4	chr3:160999064..161000624-chr3:161143841..161146775,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction
ENSG00000240567	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1017799	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12486069	0.87[ASN][1000 genomes]
rs12489004	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12489125	0.87[ASN][1000 genomes]
rs12490149	1.00[ASN][1000 genomes]
rs12494520	0.82[AMR][1000 genomes]
rs12494725	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12496235	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs13315320	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13319558	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13319771	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16831850	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16831864	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16831882	0.87[ASN][1000 genomes]
rs16831942	0.87[ASN][1000 genomes]
rs2306209	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28451189	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28704960	0.87[ASN][1000 genomes]
rs28713364	0.91[AMR][1000 genomes]
rs3925722	0.81[ASN][1000 genomes]
rs4296611	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4352387	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4468992	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4580574	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4635725	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57903480	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59567999	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59757775	0.90[ASN][1000 genomes]
rs59776766	0.87[ASN][1000 genomes]
rs60121330	0.87[ASN][1000 genomes]
rs6441350	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6441363	0.88[AMR][1000 genomes]
rs6441365	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6441372	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6441375	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6762064	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6774919	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6775446	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6775931	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6778186	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6781086	0.85[AMR][1000 genomes]
rs6782415	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6782518	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6785714	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6787447	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6787697	0.80[AMR][1000 genomes]
rs6788738	0.91[AMR][1000 genomes]
rs6790805	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6793980	0.83[AMR][1000 genomes]
rs6796168	0.87[ASN][1000 genomes]
rs6801664	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6805976	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73017340	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026933	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs73026967	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026968	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026983	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026987	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026989	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73878309	0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7615833	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7615868	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7624791	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7626773	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7634299	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7651924	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7652624	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9290070	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9290071	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9810351	0.87[ASN][1000 genomes]
rs9812574	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9818470	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9818835	0.87[ASN][1000 genomes]
rs9818992	0.82[ASN][1000 genomes]
rs9819793	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9822705	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9822916	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9823424	0.87[ASN][1000 genomes]
rs9824535	0.87[ASN][1000 genomes]
rs9824805	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826857	0.87[ASN][1000 genomes]
rs9830183	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9833270	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9834806	0.88[AMR][1000 genomes]
rs9835530	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9838945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9841871	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9847842	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9851699	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9855112	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9855572	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9856742	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858907	0.87[ASN][1000 genomes]
rs9859641	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9860980	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9862867	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9871753	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9876077	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9877309	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880536	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9884100	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9985364	0.94[AMR][1000 genomes];0.97[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	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
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv829770	chr3:160989573-161069223	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160984800-161002400	Weak transcription	NHEK	skin
2	chr3:160989000-161000400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:160994600-161002200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr3:160994600-161016800	Weak transcription	Right Ventricle	heart
5	chr3:160997400-161002200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:161000000-161000400	Active TSS	Esophagus	oesophagus

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