Variant report

Variant	rs61416782
Chromosome Location	chr20:25488724-25488725
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:25476255..25479902-chr20:25487059..25491596,6	MCF-7	breast:
2	chr20:25487824..25490513-chr20:25503941..25506270,3	MCF-7	breast:
3	chr20:25477682..25478236-chr20:25488620..25489236,2	MCF-7	breast:
4	chr20:25487968..25491385-chr20:25492316..25494168,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101004	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11087514	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28565216	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28714346	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35054550	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57273246	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57284766	1.00[AMR][1000 genomes]
rs57365695	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57734297	1.00[AMR][1000 genomes]
rs57956383	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58167480	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58476027	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59002519	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59107453	1.00[AMR][1000 genomes]
rs59124158	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59366271	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59444992	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59512557	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs59802545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59813927	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59846731	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59887855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59894298	1.00[AMR][1000 genomes]
rs60054780	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60505561	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61170040	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7261761	1.00[AMR][1000 genomes]
rs7264886	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7265940	1.00[AMR][1000 genomes]
rs7266057	1.00[AMR][1000 genomes]
rs7272899	1.00[AMR][1000 genomes]
rs8124309	0.83[AMR][1000 genomes]
rs8126155	0.85[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	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
2	nsv1056997	chr20:25316663-25492339	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS ZNF genes & repeats 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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25446000-25489600	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr20:25448200-25490600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr20:25451400-25488800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr20:25453400-25494400	Strong transcription	Brain Germinal Matrix	brain
5	chr20:25457800-25489000	Weak transcription	Placenta	Placenta
6	chr20:25459800-25489800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr20:25465600-25490000	Weak transcription	Brain Angular Gyrus	brain
8	chr20:25467400-25491800	Weak transcription	Primary T cells from cord blood	blood
9	chr20:25473400-25494400	Strong transcription	Fetal Brain Female	brain
10	chr20:25473600-25494600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr20:25473600-25494600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr20:25473800-25494200	Strong transcription	Thymus	Thymus
13	chr20:25474400-25495200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr20:25474600-25494800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr20:25474800-25493400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr20:25475400-25494000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr20:25475400-25498000	Weak transcription	Right Ventricle	heart
18	chr20:25477000-25494800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr20:25477400-25495200	Strong transcription	H9 Cell Line	embryonic stem cell
20	chr20:25478200-25494800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr20:25478400-25490000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr20:25478800-25490400	Weak transcription	Fetal Thymus	thymus
23	chr20:25478800-25494600	Strong transcription	Fetal Muscle Leg	muscle
24	chr20:25480400-25494600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr20:25480800-25494600	Strong transcription	Fetal Lung	lung
26	chr20:25481200-25494000	Strong transcription	Dnd41	blood
27	chr20:25481400-25494800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr20:25482200-25488800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr20:25482600-25494600	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr20:25483000-25494400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr20:25483000-25494800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr20:25483400-25494600	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr20:25484600-25489000	Weak transcription	Esophagus	oesophagus
34	chr20:25484600-25489200	Weak transcription	NHLF	lung
35	chr20:25484800-25489600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr20:25485000-25490600	Weak transcription	Left Ventricle	heart
37	chr20:25485400-25489400	Weak transcription	Adipose Nuclei	Adipose
38	chr20:25485400-25489400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr20:25485600-25489000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr20:25485600-25489400	Weak transcription	Aorta	Aorta
41	chr20:25485800-25489400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr20:25485800-25494800	Strong transcription	Fetal Stomach	stomach
43	chr20:25485800-25498600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr20:25486000-25489400	Weak transcription	Colon Smooth Muscle	Colon
45	chr20:25486200-25489600	Genic enhancers	Fetal Intestine Large	intestine
46	chr20:25487200-25489400	Enhancers	Fetal Intestine Small	intestine
47	chr20:25487200-25491600	Strong transcription	Fetal Brain Male	brain
48	chr20:25487200-25495000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr20:25487200-25498200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr20:25487400-25489400	Weak transcription	Brain Substantia Nigra	brain

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