Variant report

Variant	rs1249781
Chromosome Location	chr1:75864529-75864530
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10158990	0.85[JPT][hapmap]
rs11163217	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11163435	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1249780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1249795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1249805	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249814	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1249815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1249822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249824	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249847	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1249849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1614816	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1739902	0.82[JPT][hapmap]
rs1778449	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1778456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1913124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2347218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2587031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2799050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6658825	0.85[JPT][hapmap]
rs6672579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6676591	0.85[JPT][hapmap]
rs6691590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs920813	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1249781	SLC44A5	cis	Thyroid	GTEx
rs1249781	SLC44A5	cis	Skin Sun Exposed Lower leg	GTEx
rs1249781	SLC44A5	cis	lung	GTEx
rs1249781	SLC44A5	cis	normal skin	skin_eQTL
rs1249781	SLC44A5	cis	Esophagus Mucosa	GTEx
rs1249781	SLC44A5	cis	uninvolved skin	skin_eQTL
rs1249781	SLC44A5	Cis_1M	lymphoblastoid	RTeQTL
rs1249781	SLC44A5	cis	lesional skin	skin_eQTL
rs1249781	SLC44A5	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75864400-75865000	Enhancers	Fetal Brain Male	brain

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