Variant report

Variant	rs12409582
Chromosome Location	chr1:210129500-210129501
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	chr1:210129000..210131185-chr1:210545129..210547627,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200972	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1040424	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs1040426	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs10489346	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10779520	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10779521	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10863800	1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs10863801	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10863806	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10863809	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs11119371	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11119372	0.97[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11119373	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs11119377	0.85[AMR][1000 genomes]
rs11119384	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11119388	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs11119391	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11119394	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs11119398	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs11119401	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11119403	0.82[AMR][1000 genomes]
rs11119417	1.00[AFR][1000 genomes]
rs12057832	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12059828	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12061641	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12064990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12065575	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12066358	1.00[AFR][1000 genomes]
rs12069592	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12073617	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12078802	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12084199	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12085177	0.95[AMR][1000 genomes]
rs12088422	1.00[AFR][1000 genomes]
rs12089327	1.00[AFR][1000 genomes]
rs12089449	1.00[AFR][1000 genomes]
rs12094309	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12094626	0.95[AMR][1000 genomes]
rs12354000	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12401574	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12403002	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12403098	1.00[AFR][1000 genomes]
rs12405519	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs12405601	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12406136	1.00[AFR][1000 genomes]
rs12407647	0.95[AMR][1000 genomes]
rs12409047	1.00[AFR][1000 genomes]
rs12409060	1.00[AFR][1000 genomes]
rs12565072	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12566105	1.00[AFR][1000 genomes]
rs12566314	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12569033	1.00[AFR][1000 genomes]
rs1387932	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17015564	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17015565	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17015566	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17015667	1.00[AFR][1000 genomes]
rs2130625	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2130629	1.00[AFR][1000 genomes]
rs28417505	1.00[AFR][1000 genomes]
rs4844501	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4844502	0.92[AMR][1000 genomes]
rs4844507	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4844509	1.00[AFR][1000 genomes]
rs4844916	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs4844923	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs4844924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4844928	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4844935	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4844936	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4844937	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4844938	0.90[AMR][1000 genomes]
rs4844939	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs4844940	0.90[AMR][1000 genomes]
rs4844941	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4844942	0.85[AMR][1000 genomes]
rs4844943	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4844944	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4844945	1.00[AFR][1000 genomes]
rs4844946	1.00[AFR][1000 genomes]
rs4844955	1.00[AFR][1000 genomes]
rs713114	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs72649912	0.92[AMR][1000 genomes]
rs72649913	0.92[AMR][1000 genomes]
rs72649914	0.90[AMR][1000 genomes]
rs72649920	0.92[AMR][1000 genomes]
rs72649921	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs72649923	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs72649924	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs72649925	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes]
rs72649937	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs72649938	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72649940	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72649948	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72649949	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs72649955	1.00[AFR][1000 genomes]
rs72649956	1.00[AFR][1000 genomes]
rs72649959	1.00[AFR][1000 genomes]
rs72649960	1.00[AFR][1000 genomes]
rs760768	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs9787400	1.00[AFR][1000 genomes]
rs9919217	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv1825811	chr1:210082206-210135806	Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:210120000-210136000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:210124000-210132000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:210126400-210130800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:210126800-210152000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:210128200-210132200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr1:210129200-210130000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links