Variant report

Variant	rs562987142
Chromosome Location	chr20:25355167-25355168
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25354700..25357442-chr20:25369809..25371480,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100997	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv833948	chr20:25231726-25410540	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv482647	chr20:25308912-25481982	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
15	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
16	nsv1061058	chr20:25327960-25388841	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
17	nsv964440	chr20:25351740-25387631	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
18	esv3417690	chr20:25354897-25360686	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25327400-25361400	Weak transcription	Primary T cells from cord blood	blood
2	chr20:25334600-25357600	Weak transcription	Fetal Muscle Leg	muscle
3	chr20:25334800-25362600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr20:25337000-25370000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr20:25337400-25355600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr20:25337600-25362800	Weak transcription	Spleen	Spleen
7	chr20:25338000-25369400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr20:25338200-25359000	Weak transcription	Fetal Intestine Large	intestine
9	chr20:25339400-25359600	Weak transcription	Lung	lung
10	chr20:25341800-25357600	Weak transcription	Ovary	ovary
11	chr20:25342200-25361800	Weak transcription	Primary B cells from cord blood	blood
12	chr20:25342200-25362600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr20:25342200-25370000	Weak transcription	Primary hematopoietic stem cells	blood
14	chr20:25342400-25355600	Weak transcription	A549	lung
15	chr20:25342400-25357600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr20:25343800-25370000	Weak transcription	Small Intestine	intestine
17	chr20:25345200-25369800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr20:25345800-25357600	Weak transcription	Right Atrium	heart
19	chr20:25345800-25359400	Weak transcription	Left Ventricle	heart
20	chr20:25345800-25359600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr20:25345800-25361600	Weak transcription	K562	blood
22	chr20:25345800-25363200	Weak transcription	Esophagus	oesophagus
23	chr20:25345800-25369800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr20:25345800-25370000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr20:25345800-25370000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr20:25346200-25357600	Weak transcription	HepG2	liver
27	chr20:25346200-25362800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr20:25346600-25355200	Weak transcription	Gastric	stomach
29	chr20:25347600-25357600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr20:25350600-25357000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr20:25351400-25357000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr20:25351400-25359800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr20:25351400-25369600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr20:25351800-25370000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr20:25352000-25356000	Weak transcription	Pancreas	Pancrea
36	chr20:25352000-25356800	Weak transcription	Brain Angular Gyrus	brain
37	chr20:25352000-25357200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr20:25352000-25359600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr20:25352000-25359600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr20:25352000-25362600	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr20:25352400-25355600	Weak transcription	Brain Substantia Nigra	brain
42	chr20:25352400-25357000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr20:25352600-25356000	Weak transcription	Brain Hippocampus Middle	brain
44	chr20:25352600-25356200	Weak transcription	Brain Anterior Caudate	brain
45	chr20:25353000-25370000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr20:25353800-25359800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr20:25353800-25361200	Weak transcription	Aorta	Aorta
48	chr20:25353800-25365200	Weak transcription	Fetal Lung	lung
49	chr20:25353800-25368800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr20:25353800-25370000	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links