Variant report

Variant	rs4238075
Chromosome Location	chr12:40165531-40165532
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	chr12:40165086..40168049-chr12:40212824..40214791,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199571	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10444571	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10444572	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747879	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784058	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238074	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238077	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4238078	0.95[EUR][1000 genomes]
rs4267135	0.95[EUR][1000 genomes]
rs4268570	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4321021	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4322462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4334098	1.00[ASN][1000 genomes]
rs4334099	1.00[ASN][1000 genomes]
rs4374002	1.00[ASN][1000 genomes]
rs4391873	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4397917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4426190	0.94[EUR][1000 genomes]
rs4427625	0.95[EUR][1000 genomes]
rs4435073	1.00[ASN][1000 genomes]
rs4441086	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4447240	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4450227	1.00[ASN][1000 genomes]
rs4511345	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4529945	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4533100	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4544077	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4576894	0.81[EUR][1000 genomes]
rs4583047	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4611277	1.00[ASN][1000 genomes]
rs4639999	0.95[EUR][1000 genomes]
rs4767953	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768173	1.00[ASN][1000 genomes]
rs4768175	1.00[ASN][1000 genomes]
rs4768176	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4768178	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768180	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768181	0.95[EUR][1000 genomes]
rs4768182	0.95[EUR][1000 genomes]
rs56122050	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581325	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581336	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581337	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581338	0.95[EUR][1000 genomes]
rs6581346	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133037	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7135021	1.00[ASN][1000 genomes]
rs7135047	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7300946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302571	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956254	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961216	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967287	1.00[ASN][1000 genomes]
rs7967347	1.00[ASN][1000 genomes]
rs7969296	0.95[EUR][1000 genomes]
rs7973782	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975209	0.95[EUR][1000 genomes]
rs9645805	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv899024	chr12:40046408-40188870	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1053603	chr12:40082673-40197609	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv427907	chr12:40122713-40199621	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv428280	chr12:40122713-40199621	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40144800-40166400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr12:40145000-40175000	Weak transcription	Right Ventricle	heart
3	chr12:40146000-40166800	Weak transcription	Ovary	ovary
4	chr12:40153200-40171400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:40156400-40172800	Weak transcription	Fetal Intestine Small	intestine
6	chr12:40158000-40173600	Weak transcription	Aorta	Aorta
7	chr12:40158200-40166400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr12:40158200-40166400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:40158200-40174400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:40158200-40179000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:40158200-40199000	Weak transcription	Left Ventricle	heart
12	chr12:40161000-40166600	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:40161600-40198800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:40165000-40167800	Enhancers	Hela-S3	cervix
15	chr12:40165200-40165600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:40165200-40165600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:40165200-40165800	Enhancers	HMEC	breast

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