Variant report

Variant	rs28961621
Chromosome Location	chr2:51889503-51889504
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17864582	0.95[AFR][1000 genomes]
rs28949278	0.80[AFR][1000 genomes]
rs28960992	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28960998	1.00[AFR][1000 genomes]
rs28961315	0.95[AFR][1000 genomes]
rs28961319	0.84[AFR][1000 genomes]
rs28961320	0.82[AFR][1000 genomes]
rs28961335	0.90[AFR][1000 genomes]
rs28961343	0.84[AFR][1000 genomes]
rs28961618	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28961625	0.97[AFR][1000 genomes]
rs28967878	0.83[AFR][1000 genomes]
rs28967884	0.81[AFR][1000 genomes]
rs28967888	0.81[AFR][1000 genomes]
rs28967890	0.81[AFR][1000 genomes]
rs58028999	1.00[AFR][1000 genomes];1.00[AMR][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	nsv1001552	chr2:51225970-52139741	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv535708	chr2:51225970-52139741	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv874069	chr2:51723107-52006583	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1011738	chr2:51731251-51976068	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv527776	chr2:51876663-51898276	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv581887	chr2:51883456-51927714	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv874072	chr2:51883456-51928042	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:51888400-51891800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:51888800-51889600	Enhancers	H9 Cell Line	embryonic stem cell
3	chr2:51889000-51889800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr2:51889000-51891200	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr2:51889200-51890600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:51889400-51889600	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr2:51889400-51889800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:51889400-51891200	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr2:51889400-51891400	Enhancers	HUES64 Cell Line	embryonic stem cell

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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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