Variant report

Variant	rs6770180
Chromosome Location	chr3:160703786-160703787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10513560	1.00[CEU][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936216	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12690576	0.82[CEU][hapmap]
rs1374786	0.89[ASN][1000 genomes]
rs1374787	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs1447608	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1447609	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530635	0.89[ASN][1000 genomes]
rs1530636	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562465	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1562466	0.89[ASN][1000 genomes]
rs1580253	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1580254	0.85[AMR][1000 genomes]
rs1868108	0.82[CEU][hapmap]
rs1868109	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2121721	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2376476	0.85[EUR][1000 genomes]
rs2376477	0.86[EUR][1000 genomes]
rs2889391	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441346	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763532	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769927	0.85[AMR][1000 genomes]
rs6774203	1.00[CEU][hapmap];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	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs733948	0.82[CEU][hapmap]
rs7611005	0.84[EUR][1000 genomes]
rs7613316	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7616249	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7626904	0.86[EUR][1000 genomes]
rs7626985	0.87[EUR][1000 genomes]
rs7635796	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7640874	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7644586	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.94[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	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs956447	0.83[CEU][hapmap]
rs9813700	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9839984	0.84[AMR][1000 genomes]
rs9840600	0.91[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9846254	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9857743	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9858335	0.85[AMR][1000 genomes]
rs9860182	0.95[CEU][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9873705	0.85[AMR][1000 genomes]
rs9881807	0.82[CEU][hapmap]

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	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
2	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
rs6770180	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160697000-160704000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:160697200-160710600	Weak transcription	Left Ventricle	heart
3	chr3:160701200-160704000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:160702800-160703800	Weak transcription	Right Atrium	heart
5	chr3:160703400-160704800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr3:160703600-160704600	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr3:160703600-160705000	Enhancers	Primary monocytes fromperipheralblood	blood

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