Variant report

Variant	rs2026998
Chromosome Location	chr9:103181596-103181597
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103179441..103181859-chr9:103182962..103185659,2	K562	blood:
2	chr9:103112367..103115104-chr9:103180612..103183941,3	K562	blood:
3	chr9:103174960..103177942-chr9:103180157..103183043,3	K562	blood:
4	chr9:103113132..103116703-chr9:103181535..103184392,3	MCF-7	breast:
5	chr9:103179513..103182499-chr9:103189400..103191115,2	K562	blood:

Variant related genes	Relation type
ENSG00000136891	Chromatin interaction
ENSG00000066697	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1016176	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1016177	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10819788	0.80[MEX][hapmap]
rs10989090	0.81[EUR][1000 genomes]
rs10989092	0.81[EUR][1000 genomes]
rs10989127	0.80[MEX][hapmap]
rs12004257	0.80[MEX][hapmap]
rs12237166	0.80[EUR][1000 genomes]
rs1332598	0.80[MEX][hapmap]
rs17740576	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17741842	0.95[GIH][hapmap];0.93[MEX][hapmap]
rs17813447	0.89[EUR][1000 genomes]
rs17813663	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17813801	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17813854	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17814243	1.00[YRI][hapmap]
rs17814768	0.81[CEU][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap]
rs17814828	0.95[GIH][hapmap];0.86[MEX][hapmap]
rs1930238	0.93[MEX][hapmap]
rs2151107	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2274882	0.80[MEX][hapmap]
rs35438121	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41274963	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4395949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56179916	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56313595	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56720423	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57241635	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58030694	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58698990	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59668196	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61306839	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61386923	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7033848	1.00[YRI][hapmap]
rs7033969	1.00[YRI][hapmap]
rs7041189	0.95[GIH][hapmap];0.93[MEX][hapmap]
rs7046659	0.87[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs72733393	0.88[EUR][1000 genomes]
rs72733395	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72733397	0.87[EUR][1000 genomes]
rs72735110	0.82[EUR][1000 genomes]
rs73655529	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655531	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655532	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655533	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655535	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655536	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655539	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655540	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655541	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655542	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655543	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655544	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655545	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655546	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655547	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655549	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655550	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655551	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655553	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655554	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7865385	0.95[GIH][hapmap];0.93[MEX][hapmap]
rs7866623	0.86[AFR][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	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2026998	C9orf30	cis	lymphoblastoid	seeQTL
rs2026998	LOC286359	cis	cerebellum	SCAN
rs2026998	C9orf30	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103174600-103188800	Weak transcription	Esophagus	oesophagus
2	chr9:103176800-103188000	Weak transcription	K562	blood
3	chr9:103180400-103188600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:103181200-103181800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:103181200-103182000	Enhancers	HSMM	muscle
6	chr9:103181400-103182000	Enhancers	HepG2	liver

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