Variant report

Variant	rs12085177
Chromosome Location	chr1:210156022-210156023
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1040424	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1040425	0.97[ASN][1000 genomes]
rs1040426	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10489346	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10779520	0.89[AMR][1000 genomes]
rs10779521	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10863800	0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10863801	0.95[AMR][1000 genomes]
rs10863806	0.89[AMR][1000 genomes]
rs10863809	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11119371	0.90[AMR][1000 genomes]
rs11119372	0.92[AMR][1000 genomes]
rs11119373	0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11119377	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11119384	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11119388	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11119391	0.95[AMR][1000 genomes]
rs11119394	0.97[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11119398	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11119401	0.86[AMR][1000 genomes]
rs11119403	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11119417	0.82[AMR][1000 genomes]
rs12057832	0.86[AMR][1000 genomes]
rs12059828	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12061641	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12064990	0.95[AMR][1000 genomes]
rs12065575	0.95[AMR][1000 genomes]
rs12069592	0.90[AMR][1000 genomes]
rs12073617	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12078802	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12079916	0.81[AMR][1000 genomes]
rs12084199	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12089327	0.82[AMR][1000 genomes]
rs12089449	0.81[AMR][1000 genomes]
rs12092527	0.82[AMR][1000 genomes]
rs12094309	0.86[AMR][1000 genomes]
rs12094626	1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12354000	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12401574	0.86[AMR][1000 genomes]
rs12403002	0.95[AMR][1000 genomes]
rs12403098	0.81[AMR][1000 genomes]
rs12405519	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12405601	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12407647	0.90[AMR][1000 genomes]
rs12408689	0.81[AMR][1000 genomes]
rs12409047	0.82[AMR][1000 genomes]
rs12409582	0.95[AMR][1000 genomes]
rs12565072	0.97[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12566105	0.81[AMR][1000 genomes]
rs12566314	0.93[AMR][1000 genomes]
rs1387932	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17015564	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17015565	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17015566	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17015667	0.81[AMR][1000 genomes]
rs2130625	0.89[AMR][1000 genomes]
rs4844501	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4844502	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4844507	0.89[AMR][1000 genomes]
rs4844509	0.81[AMR][1000 genomes]
rs4844916	0.92[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4844923	0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4844924	0.95[AMR][1000 genomes]
rs4844928	0.98[AMR][1000 genomes]
rs4844935	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4844936	0.95[AMR][1000 genomes]
rs4844937	0.97[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4844938	0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4844939	0.97[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4844940	0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4844941	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4844942	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4844943	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4844944	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4844946	0.81[AMR][1000 genomes]
rs713114	0.97[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs72649912	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72649913	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72649914	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs72649920	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72649921	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72649923	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72649924	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72649925	0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72649937	0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72649938	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72649940	0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72649948	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72649949	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72649955	0.82[AMR][1000 genomes]
rs760768	0.97[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9787400	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873140	chr1:210068117-210335644	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv1821002	chr1:210108473-210291476	ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12085177	CUL3	trans	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210146600-210160400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:210153200-210158800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:210153400-210157200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:210153600-210157200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:210156000-210156200	Enhancers	Fetal Brain Female	brain

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