Variant report

Variant	rs1438544
Chromosome Location	chr3:105052776-105052777
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12497260	0.81[AMR][1000 genomes]
rs13065937	0.86[CHB][hapmap]
rs13070790	0.90[CHB][hapmap]
rs13075944	0.86[CHB][hapmap]
rs13079517	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs13085657	0.85[CHB][hapmap]
rs13092913	0.86[CHB][hapmap]
rs13095216	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13095274	0.80[ASN][1000 genomes]
rs1438546	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1438549	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs1438551	0.86[CHB][hapmap]
rs1438553	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1438554	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16851175	0.86[CHB][hapmap]
rs2399046	0.91[CHB][hapmap]
rs4589964	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4894926	0.86[CHB][hapmap]
rs55934921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62262153	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6437579	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6437582	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6437583	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6437584	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6773531	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6793758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6797259	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804633	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7611398	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7620029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7620713	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7626665	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7634168	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7635959	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9288801	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs976530	0.91[CHB][hapmap]
rs9852729	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9869867	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9880342	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9883403	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007243	chr3:104833483-105063375	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1438544	GUCA1C	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105047400-105053200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:105047600-105053000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:105047800-105053200	Weak transcription	NHEK	skin
4	chr3:105052600-105054000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:105052600-105054200	Enhancers	Monocytes-CD14+_RO01746	blood

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