Variant report

Variant	rs28465616
Chromosome Location	chr4:56966174-56966175
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10001537	0.84[EUR][1000 genomes]
rs10002513	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015524	0.84[EUR][1000 genomes]
rs13121935	0.93[AFR][1000 genomes]
rs1531586	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2045982	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28426986	0.96[AFR][1000 genomes]
rs34771783	0.93[AFR][1000 genomes]
rs4142	0.96[AFR][1000 genomes]
rs4864568	0.93[AFR][1000 genomes]
rs6836927	0.93[AFR][1000 genomes]
rs6849646	0.93[AFR][1000 genomes]
rs73240536	1.00[ASN][1000 genomes]
rs9994190	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9994666	0.82[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2755990	chr4:56317136-57143037	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005845	chr4:56522075-56980357	Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv999328	chr4:56942917-57041586	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1007114	chr4:56942917-57055381	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1012036	chr4:56963544-57106642	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:56948800-56972200	Weak transcription	Fetal Stomach	stomach
2	chr4:56952000-57024400	Weak transcription	Fetal Intestine Small	intestine
3	chr4:56952800-56968400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:56952800-56978200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr4:56957600-56971800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:56962000-56968200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr4:56962400-56966800	Weak transcription	Fetal Brain Female	brain
8	chr4:56963800-56974600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:56964400-56969400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr4:56965200-56966200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr4:56965200-56966200	Enhancers	Brain Anterior Caudate	brain
12	chr4:56965200-56967800	Enhancers	Brain Germinal Matrix	brain
13	chr4:56965400-56966800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr4:56965800-56974000	Weak transcription	Primary hematopoietic stem cells	blood
15	chr4:56966000-56966200	Enhancers	Fetal Brain Male	brain
16	chr4:56966000-56971600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:56966000-56973200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:56966000-56973800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:56966000-56981200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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