Variant report

Variant	rs28729669
Chromosome Location	chr4:55563683-55563684
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11726190	0.87[ASN][1000 genomes]
rs17240054	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237017	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2237019	0.80[EUR][1000 genomes]
rs2237020	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237021	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2237023	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2282775	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2537866	0.81[EUR][1000 genomes]
rs2537867	0.81[EUR][1000 genomes]
rs2703461	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2703488	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2855770	0.81[EUR][1000 genomes]
rs2855777	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3020821	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3020825	0.83[EUR][1000 genomes]
rs3020826	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3111791	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111795	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3111800	0.82[EUR][1000 genomes]
rs3134884	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3134885	0.83[EUR][1000 genomes]
rs34332764	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796772	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56295037	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6810872	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55545600-55575800	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr4:55554600-55566400	Weak transcription	NH-A	brain
3	chr4:55555200-55573600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:55555600-55574400	Weak transcription	Fetal Stomach	stomach
5	chr4:55557800-55564200	Weak transcription	NHDF-Ad	bronchial
6	chr4:55557800-55594000	Weak transcription	Aorta	Aorta
7	chr4:55558200-55564400	Weak transcription	Fetal Thymus	thymus
8	chr4:55559600-55563800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr4:55559600-55569600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:55560000-55566200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:55560200-55564000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:55560400-55568400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr4:55561000-55606600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr4:55561200-55569200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr4:55561400-55572000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:55561600-55564400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:55561600-55567000	Strong transcription	Primary hematopoietic stem cells	blood
18	chr4:55561800-55565000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:55562000-55566400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr4:55562000-55577200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr4:55562400-55563800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr4:55562400-55564600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:55562400-55566200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:55562800-55597400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr4:55563200-55565000	Strong transcription	Ovary	ovary
26	chr4:55563200-55573400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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