Variant report

Variant	rs16831868
Chromosome Location	chr3:160795541-160795542
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160282940..160285102-chr3:160793372..160795590,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMD3-1	chr3:160792441-160796690	NONHSAT093004

Variant related genes	Relation type
ENSG00000186432	Chromatin interaction
ENSG00000229320	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1045448	1.00[CEU][hapmap];0.84[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11922296	0.84[CEU][hapmap]
rs12107243	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12488621	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12494133	0.94[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13319969	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13325518	0.89[CEU][hapmap]
rs1348976	0.81[CEU][hapmap]
rs1374789	0.83[CEU][hapmap]
rs1374790	0.82[CEU][hapmap]
rs1447615	0.84[CEU][hapmap]
rs1599380	0.88[EUR][1000 genomes]
rs1599384	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1839018	0.89[CEU][hapmap]
rs1947686	0.95[CEU][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs2231252	1.00[CEU][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2279106	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]
rs28623696	0.98[EUR][1000 genomes]
rs35440670	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35599916	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4339146	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4443220	0.95[CEU][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs4465984	0.89[CEU][hapmap];0.87[YRI][hapmap];0.88[EUR][1000 genomes]
rs6441352	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441353	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs6763838	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6795977	1.00[CEU][hapmap];0.86[YRI][hapmap];0.86[EUR][1000 genomes]
rs68159406	0.88[EUR][1000 genomes]
rs721657	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs731363	0.84[CEU][hapmap]
rs7429731	0.95[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7630896	0.93[CEU][hapmap];0.86[YRI][hapmap];0.88[EUR][1000 genomes]
rs7634115	0.88[EUR][1000 genomes]
rs7649954	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs898683	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs898684	0.95[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs898685	0.94[CEU][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9813136	0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9824308	0.95[CEU][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9829882	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9830139	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9834751	0.88[EUR][1000 genomes]
rs9836074	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9840389	0.89[EUR][1000 genomes]
rs9846316	0.83[CEU][hapmap]
rs9851292	0.84[EUR][1000 genomes]
rs9861850	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9864145	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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
rs16831868	B3GALNT1	cis	Artery Tibial	GTEx

Chromatin state (count:29 , 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	chr3:160781800-160798200	Weak transcription	Fetal Stomach	stomach
4	chr3:160781800-160822000	Weak transcription	Thymus	Thymus
5	chr3:160782000-160799800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr3:160784200-160799000	Weak transcription	Ovary	ovary
7	chr3:160787000-160822000	Weak transcription	Primary T cells from cord blood	blood
8	chr3:160787200-160818800	Weak transcription	Brain Germinal Matrix	brain
9	chr3:160787600-160803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:160788000-160799600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:160788000-160799600	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:160788000-160802800	Weak transcription	Fetal Kidney	kidney
13	chr3:160788200-160803400	Weak transcription	Fetal Brain Female	brain
14	chr3:160788600-160803400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr3:160788600-160807600	Weak transcription	Pancreas	Pancrea
16	chr3:160788800-160799400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:160788800-160803400	Weak transcription	Adipose Nuclei	Adipose
18	chr3:160789200-160799600	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:160789200-160803200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:160789600-160818800	Weak transcription	Esophagus	oesophagus
21	chr3:160789800-160798400	Weak transcription	Left Ventricle	heart
22	chr3:160789800-160802600	Weak transcription	Osteobl	bone
23	chr3:160790000-160798400	Weak transcription	Right Atrium	heart
24	chr3:160792800-160803200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:160794800-160800600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr3:160795200-160796000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:160795200-160796000	Enhancers	GM12878-XiMat	blood
28	chr3:160795200-160796200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr3:160795400-160798800	Weak transcription	Right Ventricle	heart

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