Variant report

Variant	rs28554047
Chromosome Location	chr5:53224791-53224792
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10036830	1.00[AMR][1000 genomes]
rs10036972	1.00[AMR][1000 genomes]
rs10041811	1.00[AMR][1000 genomes]
rs10042258	1.00[AMR][1000 genomes]
rs10042795	1.00[AMR][1000 genomes]
rs10042859	1.00[AMR][1000 genomes]
rs10042864	1.00[AMR][1000 genomes]
rs10043716	1.00[AMR][1000 genomes]
rs10043965	1.00[AMR][1000 genomes]
rs10044530	1.00[AMR][1000 genomes]
rs10044698	1.00[AMR][1000 genomes]
rs10045943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10052240	1.00[AMR][1000 genomes]
rs10052796	1.00[AMR][1000 genomes]
rs10060723	1.00[AMR][1000 genomes]
rs10062219	1.00[AMR][1000 genomes]
rs10062710	1.00[AMR][1000 genomes]
rs10062845	1.00[AMR][1000 genomes]
rs10063636	1.00[AMR][1000 genomes]
rs10066952	1.00[AMR][1000 genomes]
rs10075461	1.00[AMR][1000 genomes]
rs10076305	1.00[AMR][1000 genomes]
rs10077213	1.00[AMR][1000 genomes]
rs10078356	1.00[AMR][1000 genomes]
rs10079598	1.00[AMR][1000 genomes]
rs10471881	1.00[AMR][1000 genomes]
rs13436340	1.00[AMR][1000 genomes]
rs28375741	1.00[AMR][1000 genomes]
rs28504340	1.00[AMR][1000 genomes]
rs28529264	1.00[AMR][1000 genomes]
rs28689956	1.00[AMR][1000 genomes]
rs9292035	1.00[AMR][1000 genomes]
rs9885002	1.00[AMR][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	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv533778	chr5:53092696-53284566	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv880713	chr5:53198059-53906103	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	nsv830299	chr5:53207020-53386600	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv598175	chr5:53213945-53230760	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv880272	chr5:53213945-53277266	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53173800-53227800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr5:53187600-53232800	Weak transcription	Primary T cells from cord blood	blood
3	chr5:53200800-53251600	Weak transcription	Primary B cells from cord blood	blood
4	chr5:53206800-53236600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr5:53213800-53225600	Weak transcription	Fetal Intestine Large	intestine
6	chr5:53213800-53235200	Weak transcription	Fetal Intestine Small	intestine
7	chr5:53214000-53238600	Weak transcription	K562	blood
8	chr5:53217000-53230400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:53217200-53244800	Weak transcription	Pancreas	Pancrea
10	chr5:53220600-53251600	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:53220800-53230000	Weak transcription	Fetal Stomach	stomach
12	chr5:53220800-53230200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:53223000-53224800	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr5:53223000-53225600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr5:53223400-53224800	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr5:53223600-53224800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr5:53223800-53224800	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr5:53223800-53225800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr5:53224000-53226600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:53224200-53225200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:53224200-53227000	Weak transcription	Fetal Kidney	kidney
22	chr5:53224200-53232400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:53224400-53224800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:53224600-53224800	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr5:53224600-53224800	Enhancers	HUES6 Cell Line	embryonic stem cell

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