Variant report

Variant	rs17762396
Chromosome Location	chr9:103902955-103902956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10119316	0.93[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1019873	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10512278	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12341807	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12352148	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1367754	1.00[CEU][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17761685	0.93[CEU][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17829436	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17829926	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1987400	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3983746	1.00[CEU][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs41274975	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4278208	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4342669	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4742806	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4743445	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4743446	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4743449	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4743450	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55672230	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55903434	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56156225	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57097151	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57409431	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58088765	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58422308	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60195477	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60390009	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61489062	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61647398	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66858224	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72741426	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72741430	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72741431	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72741437	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72741438	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72741439	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72741444	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72741445	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72741449	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs72741452	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7852006	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831671	chr9:103858107-104020816	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv948791	chr9:103893030-103964650	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv466443	chr9:103895161-103923185	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv614961	chr9:103895161-103923185	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17762396	C9orf125	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103899000-103904400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr9:103902600-103903200	Enhancers	Fetal Brain Female	brain
3	chr9:103902800-103903400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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