Variant report

Variant	rs9840389
Chromosome Location	chr3:160799057-160799058
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160797537..160800169-chr3:160939583..160942186,2	K562	blood:
2	chr3:160792949..160795432-chr3:160798815..160800745,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271052	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1045448	0.97[EUR][1000 genomes]
rs12107243	0.89[EUR][1000 genomes]
rs12488621	0.87[EUR][1000 genomes]
rs12494133	0.81[EUR][1000 genomes]
rs13314089	0.82[ASN][1000 genomes]
rs13319969	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13320863	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1599380	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1599384	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599391	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16831868	0.89[EUR][1000 genomes]
rs1947685	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1947686	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2231252	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279106	0.89[EUR][1000 genomes]
rs28623696	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35152606	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35440670	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35446590	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35599916	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36105583	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4339146	0.87[EUR][1000 genomes]
rs4443220	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4465984	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441352	0.89[EUR][1000 genomes]
rs6441353	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6763838	0.88[EUR][1000 genomes]
rs6795977	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68159406	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs721657	0.89[EUR][1000 genomes]
rs731363	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7429731	0.87[EUR][1000 genomes]
rs7630896	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7634115	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7649954	0.88[EUR][1000 genomes]
rs898683	0.88[EUR][1000 genomes]
rs898684	0.88[EUR][1000 genomes]
rs898685	0.88[EUR][1000 genomes]
rs9290067	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9290068	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9810737	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9813136	0.94[EUR][1000 genomes]
rs9817747	0.85[ASN][1000 genomes]
rs9818516	0.82[EUR][1000 genomes]
rs9824308	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9824501	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9828205	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9829882	0.97[EUR][1000 genomes]
rs9830139	0.97[EUR][1000 genomes]
rs9834751	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9836074	0.82[EUR][1000 genomes]
rs9851292	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9861850	0.99[EUR][1000 genomes]
rs9862258	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9864145	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9840389	B3GALNT1	cis	Artery Tibial	GTEx

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160780800-160821400	Weak transcription	Fetal Brain Male	brain
2	chr3:160781400-160803400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:160781800-160822000	Weak transcription	Thymus	Thymus
4	chr3:160782000-160799800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:160787000-160822000	Weak transcription	Primary T cells from cord blood	blood
6	chr3:160787200-160818800	Weak transcription	Brain Germinal Matrix	brain
7	chr3:160787600-160803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:160788000-160799600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:160788000-160799600	Weak transcription	Fetal Muscle Leg	muscle
10	chr3:160788000-160802800	Weak transcription	Fetal Kidney	kidney
11	chr3:160788200-160803400	Weak transcription	Fetal Brain Female	brain
12	chr3:160788600-160803400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr3:160788600-160807600	Weak transcription	Pancreas	Pancrea
14	chr3:160788800-160799400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr3:160788800-160803400	Weak transcription	Adipose Nuclei	Adipose
16	chr3:160789200-160799600	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:160789200-160803200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:160789600-160818800	Weak transcription	Esophagus	oesophagus
19	chr3:160789800-160802600	Weak transcription	Osteobl	bone
20	chr3:160792800-160803200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:160794800-160800600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:160796000-160799400	Weak transcription	GM12878-XiMat	blood
23	chr3:160796000-160817400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:160796200-160799400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:160796200-160821800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr3:160796600-160803400	Weak transcription	Fetal Intestine Large	intestine
27	chr3:160797000-160822000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:160797400-160800600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:160797600-160817200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr3:160798200-160800400	Strong transcription	Fetal Stomach	stomach
31	chr3:160798400-160800200	Enhancers	Fetal Heart	heart
32	chr3:160798400-160800400	Enhancers	Left Ventricle	heart
33	chr3:160798400-160800400	Enhancers	Right Atrium	heart
34	chr3:160798600-160803600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:160798600-160821800	Weak transcription	Brain Angular Gyrus	brain
36	chr3:160798800-160799200	Enhancers	Lung	lung
37	chr3:160798800-160799400	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr3:160798800-160804200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:160799000-160799400	Weak transcription	Right Ventricle	heart
40	chr3:160799000-160799600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr3:160799000-160799600	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr3:160799000-160799600	Enhancers	Ovary	ovary
43	chr3:160799000-160800400	Enhancers	Primary hematopoietic stem cells	blood

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