Variant report

Variant	rs28623696
Chromosome Location	chr3:160789925-160789926
allele	A/G/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	chr3:160746924..160750622-chr3:160787755..160791172,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196542	Chromatin interaction
ENSG00000169255	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1045448	0.90[EUR][1000 genomes]
rs12107243	0.98[EUR][1000 genomes]
rs12488621	0.95[EUR][1000 genomes]
rs12494133	0.89[EUR][1000 genomes]
rs13319969	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1599380	0.86[EUR][1000 genomes]
rs1599384	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16831868	0.98[EUR][1000 genomes]
rs1947685	0.82[AMR][1000 genomes]
rs1947686	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2231252	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2279106	0.98[EUR][1000 genomes]
rs35152606	0.82[AMR][1000 genomes]
rs35440670	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35446590	0.82[AMR][1000 genomes]
rs35599916	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36105583	0.82[AMR][1000 genomes]
rs4339146	0.95[EUR][1000 genomes]
rs4443220	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4465984	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441352	0.98[EUR][1000 genomes]
rs6441353	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6763838	0.97[EUR][1000 genomes]
rs6795977	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs68159406	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs721657	0.98[EUR][1000 genomes]
rs7429731	0.95[EUR][1000 genomes]
rs7630896	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7634115	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7649954	0.97[EUR][1000 genomes]
rs898683	0.97[EUR][1000 genomes]
rs898684	0.97[EUR][1000 genomes]
rs898685	0.97[EUR][1000 genomes]
rs9813136	0.81[EUR][1000 genomes]
rs9824308	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9828205	0.82[AMR][1000 genomes]
rs9829882	0.90[EUR][1000 genomes]
rs9830139	0.90[EUR][1000 genomes]
rs9834751	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9840389	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9851292	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9861850	0.86[EUR][1000 genomes]
rs9864145	0.98[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
rs28623696	B3GALNT1	cis	Artery Tibial	GTEx

Chromatin state (count:34 , 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	chr3:160784200-160799000	Weak transcription	Ovary	ovary
9	chr3:160786600-160790000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr3:160787000-160822000	Weak transcription	Primary T cells from cord blood	blood
11	chr3:160787200-160818800	Weak transcription	Brain Germinal Matrix	brain
12	chr3:160787600-160803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:160788000-160799600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:160788000-160799600	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:160788000-160802800	Weak transcription	Fetal Kidney	kidney
16	chr3:160788200-160792400	Weak transcription	Hela-S3	cervix
17	chr3:160788200-160803400	Weak transcription	Fetal Brain Female	brain
18	chr3:160788600-160790400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:160788600-160791800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:160788600-160803400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:160788600-160807600	Weak transcription	Pancreas	Pancrea
22	chr3:160788800-160790400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:160788800-160799400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:160788800-160803400	Weak transcription	Adipose Nuclei	Adipose
25	chr3:160789000-160790000	Weak transcription	Dnd41	blood
26	chr3:160789200-160799600	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:160789200-160803200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:160789600-160790000	Enhancers	Right Atrium	heart
29	chr3:160789600-160790200	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr3:160789600-160793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr3:160789600-160818800	Weak transcription	Esophagus	oesophagus
32	chr3:160789800-160790000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:160789800-160798400	Weak transcription	Left Ventricle	heart
34	chr3:160789800-160802600	Weak transcription	Osteobl	bone

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