Variant report

Variant	rs58186643
Chromosome Location	chr2:144714197-144714198
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:144714032-144714441	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:144711849..144715713-chr2:144717627..144720875,3	K562	blood:
2	chr2:144714184..144715713-chr2:144719335..144720875,2	K562	blood:

Variant related genes	Relation type
GTDC1	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12612842	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12618509	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619798	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12621041	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823361	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823373	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16823382	1.00[ASN][1000 genomes]
rs1864245	0.85[ASN][1000 genomes]
rs2111671	0.99[ASN][1000 genomes]
rs28679451	0.86[ASN][1000 genomes]
rs35790422	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755088	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820756	0.86[ASN][1000 genomes]
rs55634187	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs56090763	0.85[ASN][1000 genomes]
rs56120346	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs56123489	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56136411	0.85[ASN][1000 genomes]
rs56166856	0.93[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs56396630	0.85[AFR][1000 genomes]
rs60305932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61202373	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72851896	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852907	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852908	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852911	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852913	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852918	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72852924	0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs72852926	0.88[ASN][1000 genomes]
rs72852929	0.88[ASN][1000 genomes]
rs72852930	0.88[ASN][1000 genomes]
rs72852932	0.88[ASN][1000 genomes]
rs72852936	0.88[ASN][1000 genomes]
rs72852938	0.88[ASN][1000 genomes]
rs72852941	0.88[ASN][1000 genomes]
rs72852947	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs72852948	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs72852967	0.86[ASN][1000 genomes]
rs72852969	0.86[ASN][1000 genomes]
rs72852985	0.86[ASN][1000 genomes]
rs73962140	0.86[AFR][1000 genomes]
rs73962146	0.89[AFR][1000 genomes]
rs73962150	0.85[AFR][1000 genomes]
rs73962160	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7572132	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs787170	0.89[ASN][1000 genomes]
rs9678811	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532755	chr2:144631279-145270874	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription 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	10 gene(s)	inside rSNPs	diseases
2	nsv1006344	chr2:144657716-145334899	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv535951	chr2:144657716-145334899	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1067624	chr2:144657717-145425705	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv531413	chr2:144657717-145425705	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:144695400-144714200	Weak transcription	Gastric	stomach
2	chr2:144696600-144717800	Weak transcription	Fetal Muscle Leg	muscle
3	chr2:144699600-144730400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr2:144700800-144719600	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:144704600-144728800	Weak transcription	Spleen	Spleen
6	chr2:144704800-144719200	Weak transcription	Primary B cells from cord blood	blood
7	chr2:144704800-144730800	Weak transcription	Left Ventricle	heart
8	chr2:144705000-144717800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:144709200-144714600	Weak transcription	Fetal Kidney	kidney
10	chr2:144711400-144717600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr2:144711800-144714800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:144712000-144715200	Enhancers	Muscle Satellite Cultured Cells	--
13	chr2:144713400-144715800	Enhancers	Fetal Brain Male	brain
14	chr2:144713400-144719600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:144713600-144715000	Weak transcription	Fetal Brain Female	brain
16	chr2:144713600-144717800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:144713600-144717800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:144713600-144717800	Weak transcription	NHEK	skin
19	chr2:144713600-144719600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:144713600-144719800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:144713600-144721000	Weak transcription	Fetal Lung	lung
22	chr2:144713600-144723400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:144713600-144780000	Weak transcription	HSMMtube	muscle
24	chr2:144713800-144717600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr2:144713800-144717600	Weak transcription	NHDF-Ad	bronchial
26	chr2:144713800-144717800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:144713800-144719800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:144713800-144725200	Weak transcription	Brain Hippocampus Middle	brain

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