Variant report

Variant	rs9832986
Chromosome Location	chr3:98486640-98486641
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	GATA3	chr3:98486622-98486676	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:98475526..98478052-chr3:98486297..98488947,2	MCF-7	breast:

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2028392	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs828597	0.81[CHB][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9832986	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL
rs9832986	OR5K3	cis	lymphoblastoid	seeQTL
rs9832986	TMEM45A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98475400-98489400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:98476400-98489400	Weak transcription	HepG2	liver
3	chr3:98477000-98490200	Enhancers	Fetal Heart	heart
4	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr3:98480800-98489400	Weak transcription	Stomach Mucosa	stomach
6	chr3:98482200-98487800	Weak transcription	Fetal Kidney	kidney
7	chr3:98482200-98495800	Weak transcription	Dnd41	blood
8	chr3:98482400-98489000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:98482400-98496000	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:98482600-98494600	Weak transcription	Aorta	Aorta
11	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
12	chr3:98482800-98497400	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:98483000-98497400	Weak transcription	Spleen	Spleen
14	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:98483600-98489000	Weak transcription	Thymus	Thymus
17	chr3:98483600-98489200	Weak transcription	Lung	lung
18	chr3:98483600-98489200	Weak transcription	Pancreas	Pancrea
19	chr3:98483600-98489200	Weak transcription	Right Atrium	heart
20	chr3:98483600-98495200	Weak transcription	Fetal Thymus	thymus
21	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
22	chr3:98483800-98487200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:98483800-98487200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr3:98483800-98487600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr3:98483800-98496400	Weak transcription	Fetal Lung	lung
26	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr3:98484000-98487200	Weak transcription	Liver	Liver
28	chr3:98484000-98488200	Weak transcription	GM12878-XiMat	blood
29	chr3:98484000-98489000	Weak transcription	Placenta	Placenta
30	chr3:98484000-98489200	Weak transcription	Psoas Muscle	Psoas
31	chr3:98484000-98498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:98484200-98487800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:98484400-98487000	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:98484600-98487200	Weak transcription	Brain Anterior Caudate	brain
37	chr3:98484600-98487200	Weak transcription	Brain Substantia Nigra	brain
38	chr3:98484600-98487600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:98484600-98487600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:98484600-98488800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:98484800-98487600	Weak transcription	Adipose Nuclei	Adipose
42	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
43	chr3:98485000-98496200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr3:98485200-98487000	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr3:98485200-98488600	Enhancers	HUVEC	blood vessel
46	chr3:98485400-98488400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:98485400-98491600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr3:98485600-98487800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr3:98486000-98487400	Weak transcription	Brain Angular Gyrus	brain
50	chr3:98486000-98488000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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