Variant report

Variant	rs3798800
Chromosome Location	chr6:133012322-133012323
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1024178	0.85[CHB][hapmap];0.90[CHD][hapmap]
rs11965817	0.85[CHB][hapmap]
rs1569653	0.90[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1569654	0.85[CHB][hapmap]
rs2064311	0.86[ASN][1000 genomes]
rs2064312	0.87[ASN][1000 genomes]
rs2267950	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2272996	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3798801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62425072	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62425075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6930032	0.84[TSI][hapmap];0.80[EUR][1000 genomes]
rs9373029	0.85[ASN][1000 genomes]
rs9375915	0.88[ASN][1000 genomes]
rs9389011	1.00[LWK][hapmap]
rs9389025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9389026	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399037	0.85[ASN][1000 genomes]
rs9399040	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	nsv532069	chr6:132776411-133462292	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv1015742	chr6:132933666-133285852	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3798800	AHI1	cis	cerebellum	SCAN
rs3798800	AHI1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:133002200-133014600	Strong transcription	Liver	Liver
2	chr6:133004800-133016400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:133008800-133016200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:133010400-133015200	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr6:133010800-133013800	Strong transcription	Duodenum Mucosa	Duodenum
6	chr6:133011000-133015200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr6:133011200-133015000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr6:133011600-133012600	Enhancers	Stomach Mucosa	stomach
9	chr6:133011600-133014200	Weak transcription	Pancreas	Pancrea
10	chr6:133011800-133017200	Weak transcription	Spleen	Spleen

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