Variant report

Variant	rs9460992
Chromosome Location	chr6:24329730-24329731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24329272..24332186-chr6:24354451..24356131,2	MCF-7	breast:
2	chr6:24327848..24330728-chr6:24332422..24334175,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12189743	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12192494	0.80[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12192603	0.89[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1923168	0.85[ASN][1000 genomes]
rs1923169	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2185597	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2328819	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4412188	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4445044	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4496795	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4541735	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4580860	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4599626	0.89[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6456605	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6904234	0.94[CHB][hapmap];0.84[ASN][1000 genomes]
rs7754567	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7759923	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7770684	0.85[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7775064	0.83[CEU][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9460994	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9467117	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[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	nsv511339	chr6:24323858-24330240	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv601159	chr6:24325627-24329730	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9460992	HFE	cis	parietal	SCAN
rs9460992	HIST1H2BO	cis	cerebellum	SCAN
rs9460992	NKAPL	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24324400-24332000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr6:24324600-24330000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:24324600-24332000	Weak transcription	HMEC	breast
4	chr6:24324600-24332200	Weak transcription	HSMMtube	muscle
5	chr6:24327400-24339200	Weak transcription	Pancreas	Pancrea
6	chr6:24329000-24329800	Enhancers	Fetal Kidney	kidney
7	chr6:24329000-24331000	Flanking Active TSS	A549	lung
8	chr6:24329000-24331200	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr6:24329200-24330800	Enhancers	NHEK	skin
10	chr6:24329400-24330000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:24329600-24330000	Enhancers	HepG2	liver
12	chr6:24329600-24332200	Weak transcription	NH-A	brain

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