Variant report

Variant	rs28551538
Chromosome Location	chr2:38887184-38887185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11688977	0.84[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11689051	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12712609	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs13387464	0.91[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3821023	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4670262	0.93[EUR][1000 genomes]
rs4670263	0.94[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4670882	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4670883	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6732137	0.98[ASN][1000 genomes]
rs6744400	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6761563	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7571326	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7574493	0.85[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7588762	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7590750	0.96[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7590835	0.90[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7590926	0.93[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7597535	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv581485	chr2:38839323-38893660	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv873883	chr2:38881106-38932777	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	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	chr2:38878200-38888400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:38882000-38887600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:38882200-38889800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:38882200-38892800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:38882400-38887600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:38882800-38891200	Weak transcription	K562	blood
7	chr2:38882800-38892800	Weak transcription	Thymus	Thymus
8	chr2:38883000-38889600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr2:38886200-38889800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:38886600-38889800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:38886600-38890200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr2:38886600-38890400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr2:38886600-38892200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr2:38886800-38890200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:38886800-38890600	Weak transcription	GM12878-XiMat	blood

Quick Search:

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

what's new

Quick links