Variant report

Variant	rs1778459
Chromosome Location	chr1:75884232-75884233
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11806471	0.80[ASN][1000 genomes]
rs12402118	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1249777	0.85[ASN][1000 genomes]
rs1249794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1249796	0.83[CHB][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1249797	0.82[CHB][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1249807	0.82[CHB][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs1249823	0.83[ASN][1000 genomes]
rs1343519	0.84[CHB][hapmap]
rs1443846	0.83[CHB][hapmap];0.87[ASN][1000 genomes]
rs1571983	0.84[JPT][hapmap]
rs17096860	0.80[ASN][1000 genomes]
rs1778454	0.83[CHB][hapmap]
rs1891902	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs211786	0.84[JPT][hapmap]
rs2347215	0.82[ASN][1000 genomes]
rs2347217	0.81[CHB][hapmap];0.84[JPT][hapmap]
rs2972005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3845363	0.80[ASN][1000 genomes]
rs6676696	0.83[JPT][hapmap]
rs74089241	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1013952	chr1:75716654-75936048	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv535004	chr1:75716654-75936048	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	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
5	esv3441748	chr1:75866980-75890018	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1011915	chr1:75879330-75934553	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1778459	SLC44A5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75883800-75889000	Weak transcription	Pancreatic Islets	Pancreatic Islet

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links