Variant report

Variant	rs12823639
Chromosome Location	chr12:42433596-42433597
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	chr12:42419273..42420906-chr12:42433551..42435383,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1074428	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11181284	0.90[ASN][1000 genomes]
rs11610892	0.94[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs11611399	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11613623	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12313210	0.90[ASN][1000 genomes]
rs12812537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12812574	0.96[EUR][1000 genomes]
rs12813181	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12819127	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12819341	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12824122	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1492364	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17224170	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17224177	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1732340	0.94[EUR][1000 genomes]
rs1872444	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs1920699	0.90[ASN][1000 genomes]
rs34064806	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34329231	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs34331898	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34619605	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34669984	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs34827386	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs34842994	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs35644702	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35682620	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs35986152	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs3990974	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4264206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4332578	0.94[EUR][1000 genomes]
rs56142563	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs58891308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61279714	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs67788023	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs68185827	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7960537	0.90[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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv832387	chr12:42345541-42465505	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv685	chr12:42420723-42434827	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42432600-42434000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:42432800-42433600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr12:42432800-42433600	Enhancers	Osteobl	bone
4	chr12:42432800-42434000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr12:42433000-42433600	Enhancers	Hela-S3	cervix
6	chr12:42433000-42433800	Enhancers	NH-A	brain
7	chr12:42433400-42434200	Enhancers	Primary B cells from peripheral blood	blood

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