Variant report

Variant	rs34462546
Chromosome Location	chr3:160698281-160698282
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10513560	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10936216	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1374786	0.88[ASN][1000 genomes]
rs1374787	0.85[EUR][1000 genomes]
rs1447608	0.93[EUR][1000 genomes]
rs1447609	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1530635	0.88[ASN][1000 genomes]
rs1530636	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1562465	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1562466	0.88[ASN][1000 genomes]
rs1580253	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1580254	0.80[AMR][1000 genomes]
rs1868109	0.81[EUR][1000 genomes]
rs2121721	0.94[EUR][1000 genomes]
rs2376476	0.84[EUR][1000 genomes]
rs2376477	0.85[EUR][1000 genomes]
rs2889391	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4608736	0.88[ASN][1000 genomes]
rs4679927	0.88[ASN][1000 genomes]
rs4679928	0.85[EUR][1000 genomes]
rs58189630	0.87[ASN][1000 genomes]
rs6441345	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441346	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6763532	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6769927	0.80[AMR][1000 genomes]
rs6770180	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6774203	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6787694	0.88[ASN][1000 genomes]
rs6798966	0.87[ASN][1000 genomes]
rs6808311	0.80[AMR][1000 genomes]
rs6808386	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7611005	0.84[EUR][1000 genomes]
rs7613316	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7616249	0.90[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7626904	0.85[EUR][1000 genomes]
rs7626985	0.86[EUR][1000 genomes]
rs7635796	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7640874	0.86[EUR][1000 genomes]
rs7644586	0.92[EUR][1000 genomes]
rs778644	0.88[ASN][1000 genomes]
rs778647	0.88[ASN][1000 genomes]
rs778650	0.88[ASN][1000 genomes]
rs778651	0.88[ASN][1000 genomes]
rs778652	0.88[ASN][1000 genomes]
rs778655	0.88[ASN][1000 genomes]
rs778656	0.88[ASN][1000 genomes]
rs778658	0.86[ASN][1000 genomes]
rs778661	0.86[ASN][1000 genomes]
rs778662	0.88[ASN][1000 genomes]
rs796610	0.88[ASN][1000 genomes]
rs814092	0.88[ASN][1000 genomes]
rs898682	0.87[EUR][1000 genomes]
rs9813700	0.93[EUR][1000 genomes]
rs9840600	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9846254	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9857743	0.93[EUR][1000 genomes]
rs9858335	0.80[AMR][1000 genomes]
rs9860182	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9873705	0.80[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
rs34462546	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 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	chr3:160687000-160698600	Weak transcription	Adipose Nuclei	Adipose
3	chr3:160695200-160698600	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr3:160695200-160701400	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr3:160696000-160700000	Enhancers	Primary B cells from cord blood	blood
6	chr3:160696200-160700600	Enhancers	Dnd41	blood
7	chr3:160697000-160704000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:160697200-160710600	Weak transcription	Left Ventricle	heart
9	chr3:160697600-160699600	Enhancers	Primary T cells from cord blood	blood
10	chr3:160697600-160700000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:160697800-160699400	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr3:160697800-160699400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr3:160697800-160699400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr3:160697800-160701400	Enhancers	Primary hematopoietic stem cells	blood
15	chr3:160698200-160699400	Enhancers	Fetal Thymus	thymus
16	chr3:160698200-160700800	Enhancers	Primary B cells from peripheral blood	blood
17	chr3:160698200-160700800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:160698200-160701000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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