Variant report

Variant	rs28416628
Chromosome Location	chr14:104514888-104514889
allele	A/G
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	GATA3	chr14:104514825-104514957	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
TDRD9	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10129730	0.81[AMR][1000 genomes]
rs10130042	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10131031	1.00[ASN][1000 genomes]
rs10131231	1.00[ASN][1000 genomes]
rs10137517	0.98[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10137676	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10137889	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10139210	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10140436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10141374	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10142365	0.81[AMR][1000 genomes]
rs10142956	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10149898	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10151165	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12436665	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2295662	1.00[ASN][1000 genomes]
rs2368996	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28439019	1.00[ASN][1000 genomes]
rs28514602	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28555097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28563863	0.81[AMR][1000 genomes]
rs28593161	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28715405	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28841005	1.00[AMR][1000 genomes]
rs4900606	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4906388	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4906393	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4906394	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4906400	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4906403	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4906407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4906412	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4906414	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55746000	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55866217	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56050561	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56279366	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56872578	1.00[ASN][1000 genomes]
rs58128911	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs58220415	1.00[ASN][1000 genomes]
rs59838226	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7150795	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74086761	0.81[AMR][1000 genomes]
rs74086783	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74086977	0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8004485	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8007491	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9324070	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9671924	0.98[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045162	chr14:104140525-104594841	Flanking Active TSS Strong transcription Bivalent Enhancer Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv542204	chr14:104140525-104594841	Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv902319	chr14:104255083-104620077	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases
4	nsv1049690	chr14:104411621-104575838	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv542208	chr14:104411621-104575838	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv526680	chr14:104427043-104568472	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1047990	chr14:104460605-104556463	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv542209	chr14:104497447-104540729	Bivalent Enhancer ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv1050479	chr14:104500427-104805738	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104492200-104516000	Weak transcription	Spleen	Spleen
2	chr14:104496400-104520800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr14:104509200-104520600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr14:104510600-104516200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr14:104510800-104521000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr14:104511800-104516200	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr14:104512800-104515000	Weak transcription	Fetal Brain Male	brain
8	chr14:104513400-104515400	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr14:104514000-104515200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr14:104514200-104516400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr14:104514200-104520000	Enhancers	HSMMtube	muscle
12	chr14:104514400-104515200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr14:104514600-104516600	Enhancers	HSMM	muscle
14	chr14:104514800-104515400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr14:104514800-104516000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr14:104514800-104516000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr14:104514800-104516600	Enhancers	Placenta Amnion	Placenta Amnion

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