Variant report

Variant	rs28477949
Chromosome Location	chr5:5363854-5363855
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10055135	1.00[AMR][1000 genomes]
rs10475297	1.00[AMR][1000 genomes]
rs12332322	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16875470	1.00[AMR][1000 genomes]
rs16875471	1.00[AMR][1000 genomes]
rs16875487	1.00[AMR][1000 genomes]
rs28535497	1.00[AMR][1000 genomes]
rs28537743	1.00[AMR][1000 genomes]
rs28647861	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2913649	1.00[AMR][1000 genomes]
rs2964420	1.00[AMR][1000 genomes]
rs9313110	1.00[AMR][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	nsv1024784	chr5:4980979-5391231	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1032719	chr5:5102763-5387406	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv537621	chr5:5102763-5387406	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:5359200-5373200	Weak transcription	Aorta	Aorta
2	chr5:5360400-5364000	Enhancers	Liver	Liver
3	chr5:5360800-5365000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:5361000-5364400	Weak transcription	Fetal Muscle Leg	muscle
5	chr5:5361600-5365000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr5:5361600-5370000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr5:5361600-5371800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:5361800-5364800	Enhancers	HepG2	liver
9	chr5:5361800-5367600	Weak transcription	Adipose Nuclei	Adipose
10	chr5:5361800-5375800	Weak transcription	Spleen	Spleen
11	chr5:5362400-5364600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:5363000-5365000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:5363000-5370200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:5363000-5370200	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:5363400-5364200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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Input of quick search could be:

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

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