Variant report

Variant	rs17303788
Chromosome Location	chr1:76005804-76005805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10493575	1.00[JPT][hapmap]
rs11578532	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs11586288	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12401888	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap]
rs12401896	1.00[JPT][hapmap]
rs12405357	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12408190	1.00[JPT][hapmap]
rs12410333	1.00[JPT][hapmap]
rs12411159	1.00[JPT][hapmap]
rs1332784	0.81[CEU][hapmap]
rs1443845	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1576927	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17303921	0.81[CEU][hapmap]
rs17375756	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17584320	1.00[JPT][hapmap]
rs17644957	1.00[JPT][hapmap]
rs184159	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs1857353	1.00[JPT][hapmap]
rs1857354	1.00[JPT][hapmap]
rs190024	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs1913118	1.00[JPT][hapmap]
rs1930323	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1936359	1.00[JPT][hapmap]
rs2024773	1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2040079	1.00[JPT][hapmap]
rs2040082	1.00[JPT][hapmap]
rs211688	1.00[JPT][hapmap]
rs211702	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs211744	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs211751	0.84[AMR][1000 genomes]
rs211752	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs211771	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs2587032	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2587040	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2748444	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2748445	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2779490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4080327	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449394	0.84[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs4540592	1.00[JPT][hapmap]
rs4949855	1.00[JPT][hapmap]
rs55694101	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61653323	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6662665	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs74091759	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74091760	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74091761	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs74091769	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7541214	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983331	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv3445096	chr1:75933216-76126980	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv2757737	chr1:75986904-76187748	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	esv2758943	chr1:75986904-76187748	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv830270	chr1:76002220-76033156	Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17303788	SLC44A5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76000000-76008600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr1:76004400-76007600	Enhancers	Fetal Intestine Small	intestine
3	chr1:76005000-76006200	Enhancers	HUVEC	blood vessel

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