Variant report

Variant	rs557355698
Chromosome Location	chr20:25390071-25390072
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr20:25389556-25390152	GM12892	blood:	n/a	n/a
2	POLR2A	chr20:25389357-25390294	HepG2	liver:	n/a	n/a
3	POLR2A	chr20:25389502-25390328	HepG2	liver:	n/a	n/a
4	POLR2A	chr20:25389347-25390078	HepG2	liver:	n/a	n/a
5	POLR2A	chr20:25389490-25390107	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr20:25389318-25390119	SK-N-MC	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:25388660..25391384-chr20:25394035..25397022,4	MCF-7	breast:
2	chr20:25369196..25373772-chr20:25386901..25390344,6	MCF-7	breast:
3	chr20:25389767..25391883-chr20:25602900..25605790,2	K562	blood:
4	chr20:25289881..25292169-chr20:25388744..25391503,2	MCF-7	breast:
5	chr20:24972013..24974485-chr20:25388171..25390084,2	MCF-7	breast:
6	chr20:25388650..25390177-chr20:25402470..25404637,3	MCF-7	breast:
7	chr20:25370156..25372734-chr20:25387934..25390472,3	MCF-7	breast:

No data

Variant related genes	Relation type
GINS1	TF binding region
ENSG00000100997	Chromatin interaction
ENSG00000101003	Chromatin interaction
ENSG00000213742	Chromatin interaction
ENSG00000101474	Chromatin interaction
ENSG00000170191	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:20 , 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	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
17	nsv1061398	chr20:25370106-25444076	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
18	nsv1059494	chr20:25377602-25441835	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
19	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
20	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

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25388600-25390400	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr20:25388800-25418000	Weak transcription	Gastric	stomach
3	chr20:25389000-25390400	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr20:25389000-25400200	Weak transcription	Stomach Mucosa	stomach
5	chr20:25389000-25433600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr20:25389200-25411000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr20:25389200-25415000	Weak transcription	Primary B cells from cord blood	blood
8	chr20:25389400-25390200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:25389400-25390200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr20:25389400-25390200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr20:25389400-25390200	Enhancers	Fetal Stomach	stomach
12	chr20:25389400-25390600	Enhancers	Duodenum Mucosa	Duodenum
13	chr20:25389400-25390600	Flanking Active TSS	HepG2	liver
14	chr20:25389400-25399400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr20:25389400-25399400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr20:25389400-25402400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr20:25389400-25407000	Weak transcription	Fetal Intestine Large	intestine
18	chr20:25389400-25407800	Weak transcription	Fetal Brain Female	brain
19	chr20:25389400-25422800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr20:25389600-25390200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr20:25389600-25390200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr20:25389600-25390200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr20:25389600-25390200	Transcr. at gene 5' and 3'	A549	lung
24	chr20:25389600-25395400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr20:25389600-25395600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr20:25389600-25397000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr20:25389600-25398000	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr20:25389600-25400800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr20:25389600-25426400	Weak transcription	NH-A	brain
30	chr20:25389600-25426600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr20:25389600-25432200	Weak transcription	Fetal Brain Male	brain
32	chr20:25389800-25390200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr20:25389800-25390200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr20:25389800-25390200	Enhancers	HMEC	breast
35	chr20:25389800-25390400	Enhancers	NHDF-Ad	bronchial
36	chr20:25389800-25391200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr20:25389800-25391600	Weak transcription	Fetal Muscle Leg	muscle
38	chr20:25389800-25393000	Weak transcription	Primary T cells from cord blood	blood
39	chr20:25389800-25396200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr20:25389800-25396400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr20:25389800-25396600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr20:25389800-25398200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr20:25389800-25398200	Weak transcription	Fetal Muscle Trunk	muscle
44	chr20:25389800-25398400	Weak transcription	Thymus	Thymus
45	chr20:25389800-25399200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr20:25389800-25399200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr20:25389800-25399400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr20:25389800-25401200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr20:25389800-25406800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr20:25389800-25411400	Weak transcription	Fetal Kidney	kidney

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