Variant report

Variant	rs57544952
Chromosome Location	chr20:25512419-25512420
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	chr20:25512408..25515336-chr20:25515482..25519858,3	MCF-7	breast:
2	chr20:25499922..25502486-chr20:25510143..25513350,3	MCF-7	breast:

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs28417591	1.00[AMR][1000 genomes]
rs56795563	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57237389	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57522322	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58189090	1.00[AMR][1000 genomes]
rs58410604	1.00[AMR][1000 genomes]
rs58722006	1.00[AMR][1000 genomes]
rs58953621	1.00[AMR][1000 genomes]
rs59362331	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59826126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60459445	1.00[AMR][1000 genomes]
rs60758360	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60772859	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60831246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60834749	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7264066	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7267807	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7270324	1.00[AMR][1000 genomes]
rs7274585	1.00[AMR][1000 genomes]
rs7274976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73331819	1.00[AMR][1000 genomes]
rs73331822	1.00[AMR][1000 genomes]
rs73331824	1.00[AMR][1000 genomes]
rs73331833	1.00[AMR][1000 genomes]
rs73331834	1.00[AMR][1000 genomes]
rs73331856	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73331880	1.00[AMR][1000 genomes]
rs73331881	1.00[AMR][1000 genomes]
rs73333506	1.00[AMR][1000 genomes]
rs73333515	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73333541	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73333553	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73333583	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73333590	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335304	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335306	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335318	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335323	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335366	1.00[AMR][1000 genomes]
rs73335383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73335402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73337316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73337317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73337328	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73337360	1.00[AMR][1000 genomes]
rs73337362	1.00[AMR][1000 genomes]
rs73337380	0.86[AFR][1000 genomes]
rs73337391	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73345082	1.00[AMR][1000 genomes]
rs73345087	1.00[AMR][1000 genomes]
rs73345088	1.00[AMR][1000 genomes]
rs73347016	1.00[AMR][1000 genomes]
rs73347023	1.00[AMR][1000 genomes]
rs73347042	1.00[AMR][1000 genomes]
rs73347058	1.00[AMR][1000 genomes]
rs73347066	1.00[AMR][1000 genomes]
rs8117413	1.00[AMR][1000 genomes]
rs8118017	1.00[AMR][1000 genomes]
rs8123947	1.00[AMR][1000 genomes]
rs9967947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats 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	24 gene(s)	inside rSNPs	diseases
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv979406	chr20:25509600-25513942	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25493200-25512800	Weak transcription	Colon Smooth Muscle	Colon
2	chr20:25493600-25513000	Weak transcription	Left Ventricle	heart
3	chr20:25495800-25519400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr20:25496000-25513200	Weak transcription	HUVEC	blood vessel
5	chr20:25497400-25514800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr20:25497600-25512600	Weak transcription	Fetal Heart	heart
7	chr20:25498200-25512600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr20:25498200-25512600	Weak transcription	Brain Anterior Caudate	brain
9	chr20:25498200-25512800	Weak transcription	Adipose Nuclei	Adipose
10	chr20:25498200-25513000	Weak transcription	Fetal Thymus	thymus
11	chr20:25498200-25514600	Weak transcription	Pancreas	Pancrea
12	chr20:25498200-25519000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr20:25498200-25519400	Weak transcription	Gastric	stomach
14	chr20:25498200-25532200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr20:25498400-25519200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr20:25498600-25512800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr20:25502600-25519800	Weak transcription	Stomach Mucosa	stomach
18	chr20:25502800-25513200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr20:25504800-25512800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr20:25505000-25512800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr20:25505200-25512800	Weak transcription	Esophagus	oesophagus
22	chr20:25505200-25513800	Weak transcription	Fetal Kidney	kidney
23	chr20:25505400-25513000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr20:25505400-25514600	Weak transcription	Lung	lung
25	chr20:25505400-25521000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr20:25507000-25512800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr20:25507200-25512600	Weak transcription	Fetal Muscle Leg	muscle
28	chr20:25507200-25513400	Weak transcription	Fetal Lung	lung
29	chr20:25507400-25512600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr20:25507400-25512600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr20:25507400-25512800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr20:25507400-25518400	Weak transcription	A549	lung
33	chr20:25507600-25512600	Weak transcription	Ovary	ovary
34	chr20:25507600-25512800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr20:25507600-25512800	Weak transcription	HMEC	breast
36	chr20:25507600-25512800	Weak transcription	Osteobl	bone
37	chr20:25507600-25513000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr20:25507600-25513400	Weak transcription	Liver	Liver
39	chr20:25507600-25513600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr20:25507600-25513600	Weak transcription	NHLF	lung
41	chr20:25507600-25518000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr20:25507600-25519600	Weak transcription	Fetal Intestine Large	intestine
43	chr20:25507800-25512800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr20:25507800-25513000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr20:25507800-25513000	Weak transcription	NH-A	brain
46	chr20:25507800-25513200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr20:25507800-25516800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr20:25509000-25513200	Weak transcription	HepG2	liver
49	chr20:25511200-25517600	Weak transcription	Fetal Brain Female	brain
50	chr20:25511200-25520200	Weak transcription	Fetal Brain Male	brain

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