Variant report

Variant	rs2889391
Chromosome Location	chr3:160696186-160696187
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10513560	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1374786	0.89[ASN][1000 genomes]
rs1374787	0.86[EUR][1000 genomes]
rs1447608	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1447609	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530635	0.89[ASN][1000 genomes]
rs1530636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562466	0.89[ASN][1000 genomes]
rs1580253	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1580254	0.85[AMR][1000 genomes]
rs1868109	0.81[EUR][1000 genomes]
rs2121721	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2376476	0.84[EUR][1000 genomes]
rs2376477	0.85[EUR][1000 genomes]
rs34462546	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34884182	0.84[AMR][1000 genomes]
rs4608736	0.87[ASN][1000 genomes]
rs4679927	0.89[ASN][1000 genomes]
rs4679928	0.85[EUR][1000 genomes]
rs58189630	0.88[ASN][1000 genomes]
rs6441345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441346	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769927	0.85[AMR][1000 genomes]
rs6770180	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774203	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6787694	0.89[ASN][1000 genomes]
rs6791375	0.83[AMR][1000 genomes]
rs6798966	0.87[ASN][1000 genomes]
rs6808311	0.85[AMR][1000 genomes]
rs6808386	0.92[EUR][1000 genomes]
rs7611005	0.85[EUR][1000 genomes]
rs7613316	0.93[EUR][1000 genomes]
rs7616249	0.94[EUR][1000 genomes]
rs7626904	0.86[EUR][1000 genomes]
rs7626985	0.86[EUR][1000 genomes]
rs7635796	0.93[EUR][1000 genomes]
rs7640874	0.86[EUR][1000 genomes]
rs7644586	0.84[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs778644	0.89[ASN][1000 genomes]
rs778647	0.89[ASN][1000 genomes]
rs778650	0.89[ASN][1000 genomes]
rs778651	0.89[ASN][1000 genomes]
rs778652	0.89[ASN][1000 genomes]
rs778655	0.89[ASN][1000 genomes]
rs778656	0.89[ASN][1000 genomes]
rs778658	0.87[ASN][1000 genomes]
rs778661	0.86[ASN][1000 genomes]
rs778662	0.89[ASN][1000 genomes]
rs796610	0.89[ASN][1000 genomes]
rs814092	0.89[ASN][1000 genomes]
rs898682	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9813700	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9839984	0.84[AMR][1000 genomes]
rs9840600	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9846254	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9857743	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9858335	0.85[AMR][1000 genomes]
rs9860182	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9873705	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1007004	chr3:160695108-160718154	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2889391	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160670400-160700400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:160678400-160697600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:160687000-160696600	Weak transcription	Right Ventricle	heart
4	chr3:160687000-160698600	Weak transcription	Adipose Nuclei	Adipose
5	chr3:160691600-160697800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:160695000-160696800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:160695200-160696200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:160695200-160696200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:160695200-160698600	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr3:160695200-160701400	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr3:160695800-160696200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr3:160695800-160696400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:160696000-160696200	Enhancers	Monocytes-CD14+_RO01746	blood
14	chr3:160696000-160696400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:160696000-160697200	Enhancers	Pancreas	Pancrea
16	chr3:160696000-160700000	Enhancers	Primary B cells from cord blood	blood

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