Variant report

Variant	rs17392097
Chromosome Location	chr3:160717708-160717709
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	chr3:160717602..160719198-chr3:160748866..160750938,2	MCF-7	breast:
2	chr3:160716783..160717748-chr3:160814285..160815262,3	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10513561	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12374096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12374192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12487156	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1345155	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17236697	0.84[EUR][1000 genomes]
rs17236711	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17826388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs17826412	0.84[EUR][1000 genomes]
rs17826418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17826424	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28713364	0.83[EUR][1000 genomes]
rs36015194	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56741972	0.84[EUR][1000 genomes]
rs57655051	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57916312	0.87[ASN][1000 genomes]
rs57974280	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58739937	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58878734	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59371901	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60811584	0.84[EUR][1000 genomes]
rs60866328	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62282277	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6441363	1.00[CEU][hapmap]
rs6766368	1.00[TSI][hapmap]
rs6773813	0.96[EUR][1000 genomes]
rs6798468	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73023224	0.83[EUR][1000 genomes]
rs9834806	0.83[EUR][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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1007004	chr3:160695108-160718154	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17392097	HPS3	trans	brain	seeQTL
rs17392097	GATAD1	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160705000-160720000	Weak transcription	Gastric	stomach
2	chr3:160716000-160718400	Enhancers	Primary T cells from cord blood	blood
3	chr3:160716800-160717800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:160716800-160718000	Enhancers	Dnd41	blood
5	chr3:160717200-160718400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:160717200-160718600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr3:160717400-160718200	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr3:160717400-160718400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:160717600-160717800	Weak transcription	Left Ventricle	heart

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