Variant report

Variant	rs7272141
Chromosome Location	chr20:25117199-25117200
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:24972394..24974020-chr20:25115894..25117641,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101474	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1108810	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1108811	0.97[ASN][1000 genomes]
rs11698226	0.81[ASN][1000 genomes]
rs11699149	0.81[ASN][1000 genomes]
rs11699614	0.98[ASN][1000 genomes]
rs12625069	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13039237	0.97[ASN][1000 genomes]
rs13043355	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13043906	0.98[ASN][1000 genomes]
rs13045280	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13045481	0.87[ASN][1000 genomes]
rs2057042	0.92[ASN][1000 genomes]
rs2103715	0.81[ASN][1000 genomes]
rs2235770	0.98[ASN][1000 genomes]
rs2892314	0.95[ASN][1000 genomes]
rs34242837	0.95[ASN][1000 genomes]
rs34631700	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35910458	0.91[ASN][1000 genomes]
rs36115891	0.81[ASN][1000 genomes]
rs4482560	0.92[ASN][1000 genomes]
rs4815374	0.93[ASN][1000 genomes]
rs6037024	0.90[ASN][1000 genomes]
rs6037025	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6037028	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6037029	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6037030	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6037031	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037032	0.93[ASN][1000 genomes]
rs6037033	0.93[ASN][1000 genomes]
rs6037034	0.93[ASN][1000 genomes]
rs6037038	0.95[ASN][1000 genomes]
rs6050341	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6050342	0.93[ASN][1000 genomes]
rs6050345	0.92[ASN][1000 genomes]
rs6050348	0.92[ASN][1000 genomes]
rs6050351	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6050353	0.93[ASN][1000 genomes]
rs6050359	0.93[ASN][1000 genomes]
rs6050370	0.91[ASN][1000 genomes]
rs6050390	0.81[ASN][1000 genomes]
rs6050397	0.81[ASN][1000 genomes]
rs6050400	0.81[ASN][1000 genomes]
rs6050403	0.81[ASN][1000 genomes]
rs6132804	0.97[ASN][1000 genomes]
rs6132810	0.98[ASN][1000 genomes]
rs6132812	0.81[ASN][1000 genomes]
rs6138492	0.90[ASN][1000 genomes]
rs6138493	0.93[ASN][1000 genomes]
rs6138496	0.98[ASN][1000 genomes]
rs6138504	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6138506	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6138510	0.98[ASN][1000 genomes]
rs6138511	0.98[ASN][1000 genomes]
rs6138519	0.81[ASN][1000 genomes]
rs6138520	0.81[ASN][1000 genomes]
rs6138521	0.81[ASN][1000 genomes]
rs6138528	0.81[ASN][1000 genomes]
rs7261718	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7270433	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7270464	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8115505	0.93[ASN][1000 genomes]
rs8119777	0.96[ASN][1000 genomes]
rs8122274	0.93[ASN][1000 genomes]
rs910101	0.98[ASN][1000 genomes]
rs910102	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
7	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
13	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25097200-25120000	Weak transcription	Right Atrium	heart
2	chr20:25114600-25117400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:25115000-25117800	Enhancers	Pancreas	Pancrea
4	chr20:25115600-25117600	Enhancers	Fetal Brain Male	brain
5	chr20:25116000-25117600	Enhancers	Fetal Muscle Leg	muscle
6	chr20:25116200-25117600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr20:25116200-25117800	Enhancers	Brain Hippocampus Middle	brain
8	chr20:25116200-25117800	Enhancers	Fetal Brain Female	brain
9	chr20:25116200-25117800	Enhancers	Stomach Smooth Muscle	stomach
10	chr20:25116400-25117200	Enhancers	Brain Germinal Matrix	brain
11	chr20:25116400-25117400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
12	chr20:25116400-25117800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr20:25116600-25117400	Enhancers	Brain Anterior Caudate	brain
14	chr20:25116600-25117400	Enhancers	Brain Substantia Nigra	brain
15	chr20:25116600-25117600	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr20:25116600-25118000	Enhancers	Brain Cingulate Gyrus	brain
17	chr20:25116600-25118400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr20:25116600-25118400	Enhancers	NHDF-Ad	bronchial
19	chr20:25116600-25118400	Enhancers	NHLF	lung
20	chr20:25116800-25117200	Enhancers	Brain Angular Gyrus	brain
21	chr20:25116800-25117400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr20:25116800-25117600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr20:25116800-25117600	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr20:25116800-25117800	Enhancers	Colon Smooth Muscle	Colon
25	chr20:25116800-25117800	Enhancers	Rectal Mucosa Donor 29	rectum
26	chr20:25116800-25117800	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr20:25116800-25117800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr20:25116800-25117800	Enhancers	HSMMtube	muscle
29	chr20:25116800-25118000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr20:25116800-25118000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr20:25116800-25118000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr20:25116800-25118200	Enhancers	HSMM	muscle
33	chr20:25116800-25118200	Enhancers	NH-A	brain
34	chr20:25116800-25118400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr20:25116800-25118400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr20:25116800-25118400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr20:25116800-25118400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:25116800-25118400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr20:25116800-25118400	Enhancers	HMEC	breast
40	chr20:25116800-25118400	Enhancers	Osteobl	bone
41	chr20:25116800-25118800	Flanking Active TSS	A549	lung
42	chr20:25117000-25118000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr20:25117000-25119600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links