Variant report

Variant	rs1599384
Chromosome Location	chr3:160800002-160800003
allele	C/T
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: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1045448	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs12107243	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs12488621	0.95[CEU][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12494133	0.95[CEU][hapmap];0.81[EUR][1000 genomes]
rs13314089	0.82[ASN][1000 genomes]
rs13318781	0.92[JPT][hapmap]
rs13319969	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13320863	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13325518	0.89[CEU][hapmap]
rs1374789	0.89[CEU][hapmap]
rs1374790	0.88[CEU][hapmap]
rs1447615	0.90[CEU][hapmap]
rs1599380	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1599391	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16831868	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1839018	0.89[CEU][hapmap]
rs1947685	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1947686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2231252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279106	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs28623696	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35152606	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35440670	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35446590	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35599916	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36105583	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4339146	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4443220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4465984	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4487256	0.83[JPT][hapmap]
rs4490410	0.92[JPT][hapmap]
rs6441352	0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6441353	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6763838	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs6795977	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68159406	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs721657	0.89[EUR][1000 genomes]
rs731363	1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7429731	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs7630896	1.00[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.92[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	0.95[CEU][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs898683	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs898684	0.95[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs898685	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs9290067	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9290068	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	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9824501	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9825118	0.92[JPT][hapmap]
rs9827833	0.84[JPT][hapmap]
rs9828189	0.84[JPT][hapmap]
rs9828205	0.85[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	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9836074	0.82[EUR][1000 genomes]
rs9840389	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846316	0.91[JPT][hapmap]
rs9851292	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9861850	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9862258	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9864145	0.89[EUR][1000 genomes]
rs9876553	0.84[JPT][hapmap]

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
rs1599384	B3GALNT1	cis	Artery Tibial	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

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	chr3:160787000-160822000	Weak transcription	Primary T cells from cord blood	blood
5	chr3:160787200-160818800	Weak transcription	Brain Germinal Matrix	brain
6	chr3:160787600-160803200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr3:160788000-160802800	Weak transcription	Fetal Kidney	kidney
8	chr3:160788200-160803400	Weak transcription	Fetal Brain Female	brain
9	chr3:160788600-160803400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:160788600-160807600	Weak transcription	Pancreas	Pancrea
11	chr3:160788800-160803400	Weak transcription	Adipose Nuclei	Adipose
12	chr3:160789200-160803200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:160789600-160818800	Weak transcription	Esophagus	oesophagus
14	chr3:160789800-160802600	Weak transcription	Osteobl	bone
15	chr3:160792800-160803200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:160794800-160800600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:160796000-160817400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:160796200-160821800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:160796600-160803400	Weak transcription	Fetal Intestine Large	intestine
20	chr3:160797000-160822000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:160797400-160800600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:160797600-160817200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:160798200-160800400	Strong transcription	Fetal Stomach	stomach
24	chr3:160798400-160800200	Enhancers	Fetal Heart	heart
25	chr3:160798400-160800400	Enhancers	Left Ventricle	heart
26	chr3:160798400-160800400	Enhancers	Right Atrium	heart
27	chr3:160798600-160803600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:160798600-160821800	Weak transcription	Brain Angular Gyrus	brain
29	chr3:160798800-160804200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:160799000-160800400	Enhancers	Primary hematopoietic stem cells	blood
31	chr3:160799200-160804200	Weak transcription	Lung	lung
32	chr3:160799400-160800200	Enhancers	Primary B cells from cord blood	blood
33	chr3:160799400-160800200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr3:160799400-160800200	Enhancers	GM12878-XiMat	blood
35	chr3:160799400-160800200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr3:160799400-160800400	Enhancers	Right Ventricle	heart
37	chr3:160799400-160800400	Enhancers	Dnd41	blood
38	chr3:160799400-160800600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:160799600-160800200	Enhancers	Fetal Thymus	thymus
40	chr3:160799600-160800400	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr3:160799600-160800400	Enhancers	Brain Anterior Caudate	brain
42	chr3:160799600-160800400	Enhancers	Brain Hippocampus Middle	brain
43	chr3:160799600-160800400	Enhancers	HUVEC	blood vessel
44	chr3:160799800-160800200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr3:160799800-160800200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:160799800-160800400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr3:160799800-160800400	Enhancers	Spleen	Spleen
48	chr3:160799800-160800600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr3:160799800-160800600	Enhancers	Stomach Smooth Muscle	stomach
50	chr3:160799800-160821800	Weak transcription	NHLF	lung

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