Variant report

Variant	rs283058
Chromosome Location	chr6:118625225-118625226
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1034247	1.00[CHB][hapmap]
rs13199882	1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap]
rs157487	0.86[ASN][1000 genomes]
rs166881	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs169465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs2050312	1.00[CHB][hapmap]
rs2356078	1.00[CHB][hapmap];0.87[CHD][hapmap]
rs281859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs281862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs281863	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs281865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs281870	0.86[ASN][1000 genomes]
rs281871	1.00[CHB][hapmap]
rs283041	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283043	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.80[LWK][hapmap]
rs283060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283064	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs283089	0.86[ASN][1000 genomes]
rs283090	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs283092	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap]
rs401172	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs406031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs429084	1.00[CHB][hapmap]
rs430538	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs444666	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs454842	1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap]
rs465226	0.85[CHD][hapmap]
rs4946332	0.86[ASN][1000 genomes]
rs7745369	1.00[CEU][hapmap]
rs928598	1.00[CEU][hapmap]
rs9387571	1.00[MEX][hapmap]
rs9489325	1.00[CEU][hapmap];0.87[CHD][hapmap]

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	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs283058	TNFRSF11B	trans	brain	seeQTL
rs283058	SLPI	trans	brain	seeQTL
rs283058	C2orf40	trans	brain	seeQTL
rs283058	ENPP6	trans	brain	seeQTL
rs283058	COCH	trans	brain	seeQTL
rs283058	SFRP2	trans	brain	seeQTL
rs283058	DUSP1	trans	brain	seeQTL
rs283058	OLFML2A	trans	brain	seeQTL
rs283058	SLC47A1	trans	brain	seeQTL
rs283058	OGN	trans	brain	seeQTL
rs283058	MGP	trans	brain	seeQTL
rs283058	FBXO32	trans	brain	seeQTL
rs283058	FGL2	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118618600-118626800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:118619200-118626400	Weak transcription	Aorta	Aorta
3	chr6:118621200-118627800	Weak transcription	Fetal Stomach	stomach
4	chr6:118621600-118627200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:118622400-118627000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:118624200-118626000	Enhancers	Colon Smooth Muscle	Colon
7	chr6:118624600-118626400	Enhancers	Rectal Smooth Muscle	rectum
8	chr6:118625000-118631600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr6:118625200-118626200	Enhancers	Fetal Heart	heart

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