Variant report

Variant	rs17235667
Chromosome Location	chr3:53405646-53405647
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53369973..53371575-chr3:53404543..53406152,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10433617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10433618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1108506	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs11551405	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17030933	0.92[EUR][1000 genomes]
rs17030934	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17234092	1.00[CHB][hapmap]
rs17234771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17306163	1.00[CHB][hapmap]
rs56654807	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58558806	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59145995	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62252819	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs62255989	0.82[AMR][1000 genomes]
rs62255993	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62255994	0.85[AMR][1000 genomes]
rs62255999	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62256000	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62256003	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62256009	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62256043	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256049	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62256050	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256053	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62256962	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256964	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256965	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256966	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256968	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256969	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257004	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257007	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257009	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257011	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257013	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780100	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805246	1.00[ASN][1000 genomes]
rs73080266	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73080271	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73080273	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73080295	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73082274	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7622159	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9826552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9830594	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs9830895	0.89[EUR][1000 genomes]
rs9846315	0.91[EUR][1000 genomes]
rs9850440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs9864057	0.83[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]

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	nsv876801	chr3:53325905-53467506	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv876802	chr3:53325905-53470863	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17235667	SFMBT1	cis	parietal	SCAN
rs17235667	PRKCD	cis	parietal	SCAN
rs17235667	TLR9	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53405000-53405800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
2	chr3:53405400-53405800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
3	chr3:53405400-53405800	Enhancers	K562	blood
4	chr3:53405600-53405800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
5	chr3:53405600-53405800	Enhancers	H9 Cell Line	embryonic stem cell
6	chr3:53405600-53405800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell

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