Variant report

Variant	rs828613
Chromosome Location	chr3:98480330-98480331
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr3:98480325-98481012	GM12878	blood:	n/a	chr3:98480691-98480700 chr3:98480688-98480701

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10470451	0.82[ASN][1000 genomes]
rs115931	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11923134	0.84[ASN][1000 genomes]
rs13315676	0.84[ASN][1000 genomes]
rs1530655	0.83[ASN][1000 genomes]
rs278363	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs278370	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs278374	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28553326	0.86[ASN][1000 genomes]
rs28707457	0.86[ASN][1000 genomes]
rs3755569	0.84[ASN][1000 genomes]
rs3755570	0.85[ASN][1000 genomes]
rs3772091	0.83[ASN][1000 genomes]
rs3821358	0.83[ASN][1000 genomes]
rs4638909	0.83[ASN][1000 genomes]
rs56976804	0.86[ASN][1000 genomes]
rs60464352	0.84[ASN][1000 genomes]
rs62278471	0.86[ASN][1000 genomes]
rs7611040	0.84[ASN][1000 genomes]
rs7614161	0.86[ASN][1000 genomes]
rs7643537	0.83[ASN][1000 genomes]
rs828589	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs828593	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs828594	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs828595	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828596	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828597	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs828599	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs828602	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs844159	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs844161	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs865474	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs893831	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs893832	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9879927	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs828613	ST3GAL6-AS1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98463400-98481600	Weak transcription	Right Ventricle	heart
2	chr3:98469600-98480600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:98469800-98480800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:98469800-98481800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:98469800-98481800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:98469800-98482200	Weak transcription	Psoas Muscle	Psoas
7	chr3:98470000-98481800	Weak transcription	Aorta	Aorta
8	chr3:98470000-98482600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:98475400-98489400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr3:98476400-98489400	Weak transcription	HepG2	liver
11	chr3:98477000-98490200	Enhancers	Fetal Heart	heart
12	chr3:98477400-98480600	Weak transcription	Primary T cells from cord blood	blood
13	chr3:98478200-98480400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr3:98478200-98480600	Weak transcription	Brain Anterior Caudate	brain
15	chr3:98478200-98481000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:98478200-98482000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr3:98478600-98480400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:98478800-98480800	Weak transcription	Brain Substantia Nigra	brain
19	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:98479000-98480600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:98479000-98480600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:98479000-98481200	Enhancers	Fetal Thymus	thymus
23	chr3:98479000-98482200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:98479000-98485800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:98479200-98480400	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:98479200-98480400	Weak transcription	Liver	Liver
27	chr3:98479200-98480600	Weak transcription	Brain Angular Gyrus	brain
28	chr3:98479200-98480600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:98479200-98481800	Weak transcription	Right Atrium	heart
30	chr3:98479200-98481800	Enhancers	HUVEC	blood vessel
31	chr3:98479200-98482800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr3:98479400-98480400	Weak transcription	Brain Hippocampus Middle	brain
33	chr3:98479400-98480600	Weak transcription	Adipose Nuclei	Adipose
34	chr3:98479600-98481600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:98479600-98484000	Enhancers	GM12878-XiMat	blood
36	chr3:98479800-98481000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr3:98480000-98480800	Enhancers	Primary hematopoietic stem cells	blood
38	chr3:98480000-98481000	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr3:98480000-98482200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr3:98480200-98480400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:98480200-98480600	Enhancers	Left Ventricle	heart
42	chr3:98480200-98480800	Weak transcription	Placenta	Placenta
43	chr3:98480200-98480800	Enhancers	Thymus	Thymus
44	chr3:98480200-98481000	Enhancers	Fetal Muscle Leg	muscle
45	chr3:98480200-98481800	Weak transcription	Dnd41	blood

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