Variant report

Variant	rs1948625
Chromosome Location	chr3:111251208-111251209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1027496	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10934099	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12631939	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13061590	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1391358	0.94[EUR][1000 genomes]
rs1391362	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1398748	0.82[JPT][hapmap]
rs1826960	0.83[ASN][1000 genomes]
rs1846178	0.82[ASN][1000 genomes]
rs1846179	0.82[ASN][1000 genomes]
rs2221065	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2276873	0.81[ASN][1000 genomes]
rs34780071	0.81[ASN][1000 genomes]
rs4682048	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4682283	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs57998235	0.81[ASN][1000 genomes]
rs6766795	0.81[ASN][1000 genomes]
rs6769311	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6769389	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6770506	0.82[ASN][1000 genomes]
rs6773012	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6786777	0.83[ASN][1000 genomes]
rs6793230	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6805275	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7653347	0.81[ASN][1000 genomes]
rs9814660	0.82[ASN][1000 genomes]

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	nsv460821	chr3:110637471-111501097	Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv591275	chr3:110637471-111501097	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv997756	chr3:111226058-111376585	Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv3946	chr3:111236035-111283038	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv591289	chr3:111246000-111251208	Enhancers Weak transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1948625	SLC35A5	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:111250400-111252400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:111250400-111253200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:111250600-111253000	Weak transcription	HSMMtube	muscle
4	chr3:111250600-111253200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:111250800-111253000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:111250800-111253400	Weak transcription	Osteobl	bone
7	chr3:111250800-111253600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr3:111251000-111253200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:111251000-111253200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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