Variant report

Variant	rs1979672
Chromosome Location	chr3:46274109-46274110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13096142	0.81[MEX][hapmap]
rs1388604	0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs36118141	0.84[ASN][1000 genomes]
rs41276529	0.86[ASN][1000 genomes]
rs41418050	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs41502550	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4683194	0.85[ASN][1000 genomes]
rs4683199	0.85[ASN][1000 genomes]
rs6441950	0.88[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6788849	0.85[ASN][1000 genomes]
rs6810232	0.85[ASN][1000 genomes]
rs71327045	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7371987	0.88[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.85[ASN][1000 genomes]
rs9839623	0.85[ASN][1000 genomes]
rs9840204	0.83[ASN][1000 genomes]
rs9877860	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1979672	CXCR6	cis	parietal	SCAN
rs1979672	ABHD5	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46264400-46276400	Weak transcription	Fetal Thymus	thymus
2	chr3:46265600-46276400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr3:46270800-46274600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr3:46270800-46274600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:46271000-46274600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr3:46271200-46277600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:46272000-46274400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:46273800-46274200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:46273800-46278600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr3:46274000-46275600	Enhancers	Spleen	Spleen

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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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