Variant report

Variant	rs1839016
Chromosome Location	chr3:160604387-160604388
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11711152	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11713093	0.82[EUR][1000 genomes]
rs11718966	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11916355	0.86[EUR][1000 genomes]
rs13071999	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13073059	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1345156	0.86[EUR][1000 genomes]
rs1447610	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1447622	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16831563	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1868105	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1868107	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2044571	0.82[EUR][1000 genomes]
rs2197700	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35257491	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4679920	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6441337	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6441338	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66872845	0.80[EUR][1000 genomes]
rs6768115	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6774725	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801444	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7641892	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs935497	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9844267	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9845943	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9857482	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9860537	0.84[EUR][1000 genomes]
rs9871801	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	esv3391648	chr3:160602299-160620598	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1839016	B3GALNT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160602200-160604600	Enhancers	Fetal Thymus	thymus
2	chr3:160602200-160604600	Enhancers	Thymus	Thymus
3	chr3:160602800-160604400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:160602800-160604400	Enhancers	Brain Angular Gyrus	brain
5	chr3:160603000-160604400	Enhancers	Psoas Muscle	Psoas
6	chr3:160603200-160604400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:160603200-160604400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:160603200-160604400	Enhancers	Adipose Nuclei	Adipose
9	chr3:160603200-160604400	Enhancers	Duodenum Mucosa	Duodenum
10	chr3:160603200-160604400	Enhancers	Left Ventricle	heart
11	chr3:160603200-160604600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:160603200-160604600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr3:160603200-160604600	Enhancers	Fetal Muscle Leg	muscle
14	chr3:160603200-160604600	Enhancers	Placenta	Placenta
15	chr3:160603400-160604400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:160603400-160604400	Enhancers	Brain Anterior Caudate	brain
17	chr3:160603600-160604400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr3:160603800-160604400	Flanking Active TSS	GM12878-XiMat	blood
19	chr3:160604000-160604400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr3:160604000-160604400	Enhancers	Fetal Stomach	stomach
21	chr3:160604000-160604400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr3:160604000-160604600	Enhancers	Brain Cingulate Gyrus	brain
23	chr3:160604000-160604600	Enhancers	Dnd41	blood
24	chr3:160604200-160604400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:160604200-160604400	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr3:160604200-160604400	Enhancers	Fetal Muscle Trunk	muscle
27	chr3:160604200-160604600	Enhancers	Brain Hippocampus Middle	brain
28	chr3:160604200-160605000	Enhancers	Skeletal Muscle Male	skeletal muscle

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