Variant report

Variant	rs9396602
Chromosome Location	chr6:15766501-15766502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:15739404..15741557-chr6:15764680..15767519,2	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11759386	0.89[ASN][1000 genomes]
rs16876927	0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16876933	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16876977	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1887604	1.00[CHB][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1927573	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1927574	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1927578	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs220888	1.00[CHB][hapmap]
rs372993	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs374876	0.98[ASN][1000 genomes]
rs387754	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs388044	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs389429	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs399391	1.00[CHB][hapmap];0.93[CHD][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap]
rs399732	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs400543	1.00[CHB][hapmap];0.89[CHD][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap]
rs401126	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs407288	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs421665	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs421918	1.00[CHB][hapmap];0.94[JPT][hapmap]
rs441539	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs443804	0.83[JPT][hapmap]
rs563398	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6906190	1.00[YRI][hapmap]
rs6933904	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9349987	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9358068	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9358071	0.88[AMR][1000 genomes]
rs9367881	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9370827	1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9370828	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9370829	0.81[AMR][1000 genomes]
rs9383075	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383076	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383077	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9383078	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9383079	1.00[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9396604	1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428136	chr6:15595640-15781241	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2762581	chr6:15763793-15774802	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv518098	chr6:15764675-15771988	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9396602	IFIT3	trans	brain	seeQTL
rs9396602	ISG20	trans	brain	seeQTL
rs9396602	MX1	trans	brain	seeQTL
rs9396602	PARP14	trans	brain	seeQTL
rs9396602	IFI44L	trans	brain	seeQTL
rs9396602	OAS3	trans	brain	seeQTL
rs9396602	MX2	trans	brain	seeQTL
rs9396602	IFI44	trans	brain	seeQTL
rs9396602	STAT1	trans	brain	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15759200-15770000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:15762200-15782000	Weak transcription	Pancreas	Pancrea
3	chr6:15764400-15768800	Weak transcription	K562	blood
4	chr6:15764800-15770200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr6:15765000-15770000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:15765000-15771000	Weak transcription	Gastric	stomach
7	chr6:15765600-15769200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr6:15766000-15766600	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr6:15766200-15766600	Enhancers	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links