Variant report

Variant	rs11907515
Chromosome Location	chr20:25222282-25222283
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	chr20:25212487..25223003-chr20:25225155..25231821,24	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100994	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11906864	0.89[AMR][1000 genomes]
rs11906892	0.89[AMR][1000 genomes]
rs2067793	1.00[EUR][1000 genomes]
rs2145125	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2180596	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2180597	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2228978	1.00[EUR][1000 genomes]
rs2387734	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28496800	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28770021	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28881233	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34299454	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41282340	1.00[EUR][1000 genomes]
rs41304802	1.00[EUR][1000 genomes]
rs41308633	1.00[EUR][1000 genomes]
rs58412968	0.83[EUR][1000 genomes]
rs58953621	0.83[EUR][1000 genomes]
rs59082275	0.83[EUR][1000 genomes]
rs6037061	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037064	1.00[EUR][1000 genomes]
rs6037068	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037070	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037071	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037073	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6037075	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050449	1.00[EUR][1000 genomes]
rs6050451	1.00[EUR][1000 genomes]
rs6050457	1.00[EUR][1000 genomes]
rs6050458	1.00[EUR][1000 genomes]
rs6050459	0.89[AMR][1000 genomes]
rs6050460	0.89[AMR][1000 genomes]
rs6050461	1.00[EUR][1000 genomes]
rs6050462	1.00[EUR][1000 genomes]
rs6050465	1.00[EUR][1000 genomes]
rs6050473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050474	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050476	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050478	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050485	0.84[AFR][1000 genomes]
rs6050486	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050487	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050488	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050490	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050492	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050493	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050494	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050495	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6050502	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050503	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050504	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050505	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6050507	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050508	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050509	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050510	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050511	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6050512	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7263527	1.00[EUR][1000 genomes]
rs7269045	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7273544	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7274919	0.83[EUR][1000 genomes]
rs73343076	0.83[EUR][1000 genomes]
rs73347016	0.83[EUR][1000 genomes]
rs73347066	0.83[EUR][1000 genomes]
rs7344105	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs736358	1.00[EUR][1000 genomes]
rs8116564	1.00[EUR][1000 genomes]
rs8118763	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8120268	1.00[EUR][1000 genomes]
rs8123947	0.83[EUR][1000 genomes]
rs8125980	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][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	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	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	nsv1066667	chr20:25133066-25238976	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
17	nsv544222	chr20:25133066-25238976	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25204200-25222800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr20:25214400-25223000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr20:25215400-25223200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr20:25215800-25222800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr20:25216000-25222800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr20:25217600-25227600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr20:25219000-25226000	Weak transcription	Colonic Mucosa	Colon
8	chr20:25219000-25227400	Weak transcription	Colon Smooth Muscle	Colon
9	chr20:25219400-25226800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr20:25219400-25226800	Weak transcription	Right Ventricle	heart
11	chr20:25219400-25227600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr20:25219400-25228000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr20:25219600-25222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr20:25219600-25227000	Weak transcription	NHDF-Ad	bronchial
15	chr20:25219800-25227400	Weak transcription	NHLF	lung
16	chr20:25220200-25227000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr20:25220400-25227400	Weak transcription	Esophagus	oesophagus
18	chr20:25220600-25226800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr20:25220600-25227200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr20:25220800-25226000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr20:25221600-25222400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr20:25221600-25222400	Enhancers	K562	blood
23	chr20:25221600-25223000	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr20:25221600-25223000	Enhancers	HepG2	liver
25	chr20:25221800-25222400	Enhancers	NH-A	brain
26	chr20:25221800-25222800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr20:25221800-25223000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr20:25221800-25224200	Weak transcription	Fetal Intestine Large	intestine
29	chr20:25221800-25225800	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr20:25221800-25226000	Weak transcription	Fetal Heart	heart
31	chr20:25221800-25226800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr20:25221800-25226800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr20:25222000-25222800	Weak transcription	NHEK	skin
34	chr20:25222000-25223000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr20:25222000-25223000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr20:25222000-25226200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr20:25222000-25226800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr20:25222000-25227000	Weak transcription	HSMM	muscle
39	chr20:25222000-25227200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr20:25222000-25227400	Weak transcription	Fetal Kidney	kidney
41	chr20:25222000-25227400	Weak transcription	HSMMtube	muscle
42	chr20:25222000-25227600	Weak transcription	Fetal Lung	lung
43	chr20:25222200-25222400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr20:25222200-25222600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr20:25222200-25222600	Weak transcription	A549	lung
46	chr20:25222200-25222600	Weak transcription	HMEC	breast

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