Variant report

Variant	rs1858627
Chromosome Location	chr1:75907718-75907719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1036950	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10747387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10874264	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10874305	0.88[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10874311	0.82[JPT][hapmap]
rs1107148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1116878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs12402118	0.81[CHD][hapmap]
rs1249784	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1249786	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12738260	0.82[JPT][hapmap]
rs1343519	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs1343520	0.88[CHB][hapmap];0.88[CHD][hapmap];0.85[ASN][1000 genomes]
rs1858628	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs1889036	0.83[JPT][hapmap]
rs1936358	1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2347214	0.94[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2587042	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];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6593575	1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6675276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap]

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	nsv1011915	chr1:75879330-75934553	Flanking Active TSS Weak transcription Enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv546581	chr1:75897055-75937429	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1858627	SLC44A5	cis	normal skin	skin_eQTL
rs1858627	SLC44A5	cis	Skin Sun Exposed Lower leg	GTEx
rs1858627	TYW3	cis	parietal	SCAN
rs1858627	SLC44A5	cis	Muscle Skeletal	GTEx
rs1858627	SNORD45B	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

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