Variant report

Variant	rs2354404
Chromosome Location	chr1:239666113-239666114
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10802769	0.83[AMR][1000 genomes]
rs10802770	0.83[AMR][1000 genomes]
rs10925900	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10925901	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10925902	0.81[ASN][1000 genomes]
rs10925905	0.81[ASN][1000 genomes]
rs11587861	0.82[ASN][1000 genomes]
rs12033290	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12048639	0.83[AMR][1000 genomes]
rs12136288	0.80[AMR][1000 genomes]
rs12728618	0.81[ASN][1000 genomes]
rs1338909	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1782350	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1938236	0.86[AMR][1000 genomes]
rs2354403	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2354405	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34584779	0.83[AMR][1000 genomes]
rs35192591	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61834724	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002301	chr1:239182255-239774393	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3373454	chr1:239495349-239670615	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv833037	chr1:239522168-239699412	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription 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 miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv549436	chr1:239632055-239678115	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription	lncRNA	n/a	inside rSNPs	diseases
7	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv549437	chr1:239659953-239677004	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239657400-239675200	Weak transcription	Ovary	ovary
2	chr1:239663000-239668600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:239664200-239666200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:239664400-239666800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:239665400-239666400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr1:239665600-239666400	Enhancers	Primary T helper memory cells from peripheral blood 2	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