Variant report

Variant	rs17538964
Chromosome Location	chr1:223463094-223463095
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223462981..223465642-chr1:223484099..223486031,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10495206	0.91[JPT][hapmap]
rs10495207	0.83[JPT][hapmap]
rs10907376	0.83[JPT][hapmap]
rs11261264	0.83[JPT][hapmap]
rs12123148	0.82[JPT][hapmap]
rs12140453	0.83[JPT][hapmap]
rs12564615	0.83[JPT][hapmap]
rs1341988	0.80[GIH][hapmap];0.91[JPT][hapmap]
rs1400959	0.91[JPT][hapmap]
rs1400961	0.85[CEU][hapmap];0.80[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs1400963	0.91[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418150	1.00[ASW][hapmap];0.85[CEU][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1418152	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1418153	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1640846	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1640849	0.81[CEU][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17161988	0.85[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs17163765	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17479856	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17480087	0.91[JPT][hapmap]
rs17480344	0.83[JPT][hapmap]
rs17517952	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518077	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518349	0.91[JPT][hapmap]
rs17518363	0.91[JPT][hapmap]
rs17539269	0.91[JPT][hapmap]
rs17539583	0.83[JPT][hapmap]
rs17576822	1.00[CEU][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17577025	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17577212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17578168	0.83[JPT][hapmap]
rs17578203	0.83[JPT][hapmap]
rs1773710	0.82[EUR][1000 genomes]
rs1773713	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1829310	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28561511	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3820596	0.85[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs61837627	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61837629	0.85[EUR][1000 genomes]
rs61837630	0.85[EUR][1000 genomes]
rs61837633	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61837634	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61837635	0.90[EUR][1000 genomes]
rs61837636	0.84[EUR][1000 genomes]
rs61837638	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61837640	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61838191	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838192	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838197	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838199	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838200	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838201	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712858	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73122234	0.91[EUR][1000 genomes]
rs7412060	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74145795	0.85[EUR][1000 genomes]
rs7518292	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885279	0.84[CEU][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs9442043	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1000039	chr1:223429733-223527845	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17538964	SUSD4	cis	cerebellum	SCAN
rs17538964	SUSD4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223440800-223465600	Weak transcription	Ovary	ovary
2	chr1:223443800-223472600	Weak transcription	Gastric	stomach
3	chr1:223459000-223474200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr1:223460800-223473400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:223461200-223469600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:223462600-223465600	Weak transcription	Primary T cells from cord blood	blood

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