Variant report

Variant	rs6593575
Chromosome Location	chr1:75936227-75936228
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1036950	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10747387	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs10874264	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10874305	1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs1107148	1.00[CEU][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1116878	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs1249784	1.00[CEU][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1249786	1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1858627	1.00[CEU][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1858628	0.94[JPT][hapmap];1.00[YRI][hapmap]
rs1889036	0.89[JPT][hapmap]
rs1936358	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2347214	0.94[CEU][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes]
rs2587042	1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6675276	1.00[CEU][hapmap];1.00[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	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	nsv546581	chr1:75897055-75937429	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv3359779	chr1:75914980-75939472	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs6593575	HEBP2	trans	lymphoblastoid	seeQTL
rs6593575	SNORD45B	cis	cerebellum	SCAN
rs6593575	TYW3	cis	parietal	SCAN
rs6593575	SLC44A5	cis	Skin Sun Exposed Lower leg	GTEx
rs6593575	SLC44A5	cis	normal skin	skin_eQTL
rs6593575	SLC44A5	cis	Muscle Skeletal	GTEx
rs6593575	SLC44A5	cis	Thyroid	GTEx
rs6593575	CRYZ	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75935800-75936800	Flanking Active TSS	K562	blood
2	chr1:75936000-75937200	Enhancers	Fetal Heart	heart

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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