Variant report

Variant	rs1249784
Chromosome Location	chr1:75893722-75893723
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1036950	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10747387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap]
rs10874264	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10874305	0.88[CHB][hapmap];0.89[JPT][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10874311	0.89[JPT][hapmap]
rs1107148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1116878	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs12022154	0.88[JPT][hapmap]
rs12048595	0.81[JPT][hapmap]
rs1249786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12738260	0.88[JPT][hapmap]
rs1343519	0.82[CHB][hapmap]
rs1343520	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs1858627	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap]
rs1858628	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs1936358	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs211699	0.81[JPT][hapmap]
rs211757	0.81[JPT][hapmap]
rs211764	0.81[JPT][hapmap]
rs2347214	0.94[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2587042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6593575	1.00[CEU][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6675276	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs910567	0.83[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	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1249784	SLC44A5	cis	Muscle Skeletal	GTEx
rs1249784	SLC44A5	cis	Skin Sun Exposed Lower leg	GTEx
rs1249784	SLC44A5	cis	Thyroid	GTEx
rs1249784	SLC44A5	cis	normal skin	skin_eQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75888800-75894600	Enhancers	Fetal Heart	heart
2	chr1:75893600-75893800	Enhancers	K562	blood

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