Variant report

Variant	rs6050212
Chromosome Location	chr20:24942838-24942839
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	chr20:24940462..24942946-chr20:24945395..24947544,2	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs127131	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182749	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883830	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883831	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064404	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179731	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256031	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227589	0.80[EUR][1000 genomes]
rs227603	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227617	0.82[EUR][1000 genomes]
rs227637	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227641	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227642	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227644	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227645	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227647	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227654	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227655	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227656	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28815609	1.00[ASN][1000 genomes]
rs3928737	1.00[ASN][1000 genomes]
rs4239751	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4429533	1.00[ASN][1000 genomes]
rs4432532	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4815358	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815359	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651048	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681373	1.00[ASN][1000 genomes]
rs6036998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037003	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6037006	1.00[ASN][1000 genomes]
rs6050123	1.00[ASN][1000 genomes]
rs6050128	1.00[ASN][1000 genomes]
rs6050199	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050214	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050244	1.00[ASN][1000 genomes]
rs6083696	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083697	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083714	0.99[EUR][1000 genomes]
rs6083718	1.00[ASN][1000 genomes]
rs6114995	1.00[ASN][1000 genomes]
rs6138432	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138433	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515552	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7352631	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761368	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765834	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8121279	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs914312	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv2762068	chr20:24908860-24974986	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv585745	chr20:24932028-25007089	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24930600-24943000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr20:24932000-24943000	Weak transcription	HSMM	muscle
3	chr20:24932000-24943400	Weak transcription	HSMMtube	muscle
4	chr20:24933800-24943800	Weak transcription	NHEK	skin
5	chr20:24934600-24943200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:24935000-24943000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr20:24935000-24943800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr20:24935000-24953600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr20:24935200-24943200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr20:24935200-24957600	Strong transcription	Liver	Liver
11	chr20:24935200-24971800	Weak transcription	K562	blood
12	chr20:24935400-24943000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr20:24935800-24945200	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr20:24936000-24955600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr20:24936200-24947400	Genic enhancers	Primary T cells fromperipheralblood	blood
16	chr20:24936200-24954400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr20:24936400-24943000	Strong transcription	Fetal Muscle Trunk	muscle
18	chr20:24936400-24947000	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr20:24936400-24954400	Strong transcription	Fetal Intestine Small	intestine
20	chr20:24936400-24954400	Strong transcription	Fetal Stomach	stomach
21	chr20:24936400-24954600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr20:24936400-24954600	Strong transcription	Brain Germinal Matrix	brain
23	chr20:24936400-24954600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr20:24936400-24954800	Strong transcription	Spleen	Spleen
25	chr20:24936400-24956000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr20:24936600-24943400	Weak transcription	Fetal Lung	lung
27	chr20:24936600-24944200	Strong transcription	Fetal Muscle Leg	muscle
28	chr20:24936600-24944400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr20:24936600-24945800	Strong transcription	Brain Hippocampus Middle	brain
30	chr20:24936600-24947200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr20:24936600-24950600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr20:24936600-24954200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr20:24936600-24954200	Strong transcription	Brain Substantia Nigra	brain
34	chr20:24936600-24954200	Strong transcription	Gastric	stomach
35	chr20:24936600-24954800	Strong transcription	Brain Anterior Caudate	brain
36	chr20:24936600-24954800	Strong transcription	Thymus	Thymus
37	chr20:24936800-24952600	Strong transcription	Placenta	Placenta
38	chr20:24936800-24954800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr20:24936800-24955000	Strong transcription	Lung	lung
40	chr20:24936800-24955400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr20:24936800-24955800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr20:24937000-24945400	Strong transcription	Fetal Brain Female	brain
43	chr20:24937000-24950600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr20:24937000-24955000	Strong transcription	Dnd41	blood
45	chr20:24937200-24954400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr20:24937200-24954400	Strong transcription	Duodenum Mucosa	Duodenum
47	chr20:24937200-24954600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr20:24937200-24954800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr20:24937200-24955000	Strong transcription	Stomach Smooth Muscle	stomach
50	chr20:24937400-24954200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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