Variant report

Variant	rs17577742
Chromosome Location	chr1:223486207-223486208
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10495206	0.84[ASW][hapmap];0.87[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1400959	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17480087	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17480344	0.84[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17518349	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17518363	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17539269	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17539583	0.84[ASW][hapmap];0.83[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17578168	0.84[ASW][hapmap];0.83[CEU][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17578203	1.00[ASW][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes]
rs61838208	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61838209	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61838210	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61838229	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61838230	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61838231	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61838238	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61838239	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61838240	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61838243	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61838250	0.84[AMR][1000 genomes]
rs9442042	1.00[AMR][1000 genomes];0.99[EUR][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	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
3	nsv518979	chr1:223468336-223488310	Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17577742	SUSD4	cis	parietal	SCAN
rs17577742	SUSD4	cis	Heart Left Ventricle	GTEx
rs17577742	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223470000-223493200	Weak transcription	Esophagus	oesophagus
2	chr1:223482200-223486600	Weak transcription	Ovary	ovary
3	chr1:223482200-223488200	Weak transcription	Fetal Thymus	thymus
4	chr1:223482200-223488600	Weak transcription	Primary T cells from cord blood	blood
5	chr1:223482200-223488600	Weak transcription	Thymus	Thymus
6	chr1:223485800-223487400	Enhancers	Stomach Smooth Muscle	stomach
7	chr1:223486000-223486800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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