Variant report

Variant	rs2279106
Chromosome Location	chr3:160789129-160789130
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160786415..160790259-chr3:161088559..161091068,4	MCF-7	breast:
2	chr3:160787939..160790136-chr3:160818386..160820468,2	MCF-7	breast:
3	chr3:160787784..160789478-chr3:161085891..161088171,2	MCF-7	breast:
4	chr3:160786404..160789728-chr3:161132273..161134989,3	MCF-7	breast:
5	chr3:160746924..160750622-chr3:160787755..160791172,3	MCF-7	breast:
6	chr3:160787358..160789426-chr3:161053808..161055852,2	MCF-7	breast:
7	chr3:160783848..160785805-chr3:160786120..160789700,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1045448	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11922296	0.89[CEU][hapmap]
rs12107243	1.00[CEU][hapmap];0.89[JPT][hapmap];0.80[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12488621	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12494133	0.95[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12494844	0.81[TSI][hapmap]
rs13318781	0.81[TSI][hapmap]
rs13319969	1.00[CEU][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs13325518	0.89[CEU][hapmap]
rs1348976	0.87[CEU][hapmap]
rs1374789	0.89[CEU][hapmap]
rs1374790	0.88[CEU][hapmap]
rs1447615	0.89[CEU][hapmap]
rs1599380	0.88[EUR][1000 genomes]
rs1599384	0.89[EUR][1000 genomes]
rs16831868	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1839018	0.89[CEU][hapmap]
rs1947686	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs2231252	1.00[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs28623696	0.98[EUR][1000 genomes]
rs35440670	0.88[EUR][1000 genomes]
rs35599916	0.88[EUR][1000 genomes]
rs4339146	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4443220	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4465984	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs6441352	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441353	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6763838	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6795977	1.00[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs6801330	0.89[CEU][hapmap]
rs68159406	0.88[EUR][1000 genomes]
rs721657	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs731363	0.84[TSI][hapmap]
rs7429731	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7630896	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7634115	0.88[EUR][1000 genomes]
rs7649954	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs898683	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs898684	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs898685	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9813136	0.81[CHB][hapmap];0.89[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9824308	0.95[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs9829882	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9830139	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9834751	0.88[EUR][1000 genomes]
rs9840389	0.89[EUR][1000 genomes]
rs9851292	0.84[EUR][1000 genomes]
rs9861850	0.82[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9864145	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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
rs2279106	B3GALNT1	cis	Artery Tibial	GTEx

Chromatin state (count:45 , 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	chr3:160781600-160791000	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:160781800-160798200	Weak transcription	Fetal Stomach	stomach
5	chr3:160781800-160822000	Weak transcription	Thymus	Thymus
6	chr3:160782000-160799800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:160782800-160795000	Weak transcription	Right Ventricle	heart
8	chr3:160784000-160789400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:160784200-160799000	Weak transcription	Ovary	ovary
10	chr3:160786600-160789600	Enhancers	HUVEC	blood vessel
11	chr3:160786600-160790000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr3:160786800-160789200	Enhancers	Primary hematopoietic stem cells	blood
13	chr3:160787000-160789400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr3:160787000-160789400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:160787000-160822000	Weak transcription	Primary T cells from cord blood	blood
16	chr3:160787200-160818800	Weak transcription	Brain Germinal Matrix	brain
17	chr3:160787600-160803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:160787800-160789200	Enhancers	Osteobl	bone
19	chr3:160787800-160789800	Enhancers	Brain Anterior Caudate	brain
20	chr3:160788000-160789600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr3:160788000-160799600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:160788000-160799600	Weak transcription	Fetal Muscle Leg	muscle
23	chr3:160788000-160802800	Weak transcription	Fetal Kidney	kidney
24	chr3:160788200-160789600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:160788200-160789600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:160788200-160792400	Weak transcription	Hela-S3	cervix
27	chr3:160788200-160803400	Weak transcription	Fetal Brain Female	brain
28	chr3:160788600-160789200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:160788600-160789400	Weak transcription	Brain Angular Gyrus	brain
30	chr3:160788600-160789400	Weak transcription	Esophagus	oesophagus
31	chr3:160788600-160789400	Weak transcription	Left Ventricle	heart
32	chr3:160788600-160789600	Weak transcription	Aorta	Aorta
33	chr3:160788600-160789600	Weak transcription	Right Atrium	heart
34	chr3:160788600-160790400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:160788600-160791800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:160788600-160803400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:160788600-160807600	Weak transcription	Pancreas	Pancrea
38	chr3:160788800-160789600	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr3:160788800-160790400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:160788800-160799400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:160788800-160803400	Weak transcription	Adipose Nuclei	Adipose
42	chr3:160789000-160789200	Enhancers	Brain Hippocampus Middle	brain
43	chr3:160789000-160789400	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr3:160789000-160789600	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr3:160789000-160790000	Weak transcription	Dnd41	blood

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