Variant report

Variant	rs6037003
Chromosome Location	chr20:24968017-24968018
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	chr20:24964453..24967113-chr20:24967610..24970437,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs127131	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182749	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883830	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883831	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064404	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2179731	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256031	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227603	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227617	0.83[EUR][1000 genomes]
rs227637	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227641	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227642	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227644	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227645	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227647	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227654	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227655	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227656	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28815609	1.00[ASN][1000 genomes]
rs3928737	1.00[ASN][1000 genomes]
rs4239751	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4429533	1.00[ASN][1000 genomes]
rs4815358	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815359	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55651048	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681373	1.00[ASN][1000 genomes]
rs6036998	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	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050211	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050212	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050214	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050244	1.00[ASN][1000 genomes]
rs6083696	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6083697	0.98[AMR][1000 genomes];1.00[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	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138433	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6515552	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7352631	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761368	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765834	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8121279	0.87[AMR][1000 genomes];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:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24935200-24971800	Weak transcription	K562	blood
2	chr20:24942000-24972400	Weak transcription	Fetal Heart	heart
3	chr20:24953600-24972000	Weak transcription	NH-A	brain
4	chr20:24957800-24972000	Weak transcription	HUVEC	blood vessel
5	chr20:24958000-24970400	Weak transcription	Fetal Brain Male	brain
6	chr20:24958000-24971800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr20:24958000-24972200	Weak transcription	Fetal Kidney	kidney
8	chr20:24960800-24971800	Weak transcription	Stomach Mucosa	stomach
9	chr20:24961400-24971800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr20:24961600-24971800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr20:24961600-24971800	Weak transcription	NHLF	lung
12	chr20:24961600-24972600	Weak transcription	Aorta	Aorta
13	chr20:24961800-24971400	Weak transcription	HMEC	breast
14	chr20:24962000-24969400	Weak transcription	NHEK	skin
15	chr20:24962000-24971800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr20:24962000-24971800	Weak transcription	Pancreas	Pancrea
17	chr20:24962200-24971200	Weak transcription	HSMM	muscle
18	chr20:24962200-24971800	Weak transcription	Esophagus	oesophagus
19	chr20:24962200-24971800	Weak transcription	NHDF-Ad	bronchial
20	chr20:24962200-24972600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr20:24962600-24968600	Weak transcription	GM12878-XiMat	blood
22	chr20:24962600-24971800	Weak transcription	HSMMtube	muscle
23	chr20:24962600-24972000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr20:24962800-24968600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr20:24962800-24970000	Weak transcription	Fetal Brain Female	brain
26	chr20:24962800-24971000	Weak transcription	Hela-S3	cervix
27	chr20:24962800-24971800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr20:24962800-24971800	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr20:24962800-24971800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr20:24962800-24971800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr20:24962800-24972000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr20:24962800-24972000	Weak transcription	Gastric	stomach
33	chr20:24962800-24972600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr20:24962800-24972600	Weak transcription	Ovary	ovary
35	chr20:24963000-24971800	Weak transcription	Fetal Lung	lung
36	chr20:24963200-24972400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr20:24963400-24968600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr20:24963400-24971000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr20:24963400-24971800	Weak transcription	Osteobl	bone
40	chr20:24963600-24969800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr20:24963600-24972000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr20:24964000-24972400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr20:24964200-24969200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr20:24964200-24970600	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr20:24964200-24971200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr20:24964200-24971400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr20:24964200-24971600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr20:24964200-24971600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr20:24964200-24971600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr20:24964200-24971800	Weak transcription	Stomach Smooth Muscle	stomach

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