Variant report

Variant	rs1796829
Chromosome Location	chr1:239661819-239661820
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12032799	1.00[AFR][1000 genomes]
rs12047701	1.00[AFR][1000 genomes]
rs1218660	0.83[EUR][1000 genomes]
rs17584748	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1782352	0.85[EUR][1000 genomes]
rs1796828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs20437	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41400047	1.00[AFR][1000 genomes]
rs58532785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58734274	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9428833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1796829	ARC	trans	brain	seeQTL
rs1796829	FOSB	trans	brain	seeQTL
rs1796829	PTGS2	trans	brain	seeQTL
rs1796829	EGR2	trans	brain	seeQTL
rs1796829	CCL4	trans	brain	seeQTL
rs1796829	NPAS4	trans	brain	seeQTL
rs1796829	FOS	trans	brain	seeQTL
rs1796829	CCL3	trans	brain	seeQTL
rs1796829	GADD45G	trans	brain	seeQTL
rs1796829	BTG2	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239647000-239665200	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:239657400-239675200	Weak transcription	Ovary	ovary
3	chr1:239658200-239662200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:239659000-239662400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:239660800-239664400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:239661400-239662400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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