Variant report

Variant	rs1440153
Chromosome Location	chr3:98489686-98489687
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	EP300	chr3:98489035-98489778	GM12878	blood:	n/a	n/a
2	NFIC	chr3:98488709-98489877	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:98489034-98489701	GM12892	blood:	n/a	n/a
4	EBF1	chr3:98489465-98489817	GM12878	blood:	n/a	n/a
5	EBF1	chr3:98489183-98489833	GM12878	blood:	n/a	n/a
6	RUNX3	chr3:98488989-98489775	GM12878	blood:	n/a	n/a
7	WRNIP1	chr3:98489228-98489729	GM12878	blood:	n/a	n/a
8	BHLHE40	chr3:98488891-98489867	GM12878	blood:	n/a	n/a
9	EBF1	chr3:98489078-98489864	GM12878	blood:	n/a	n/a
10	BRCA1	chr3:98489309-98489771	GM12878	blood:	n/a	n/a
11	IKZF1	chr3:98489063-98489813	GM12878	blood:	n/a	n/a
12	POLR2A	chr3:98489053-98489739	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
ST3GAL6	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1062196	0.97[GIH][hapmap];0.84[TSI][hapmap]
rs1440150	0.97[GIH][hapmap];0.86[TSI][hapmap]
rs1440152	0.83[CHB][hapmap];0.85[AMR][1000 genomes]
rs2119187	0.94[GIH][hapmap];0.84[TSI][hapmap]
rs2119188	0.89[GIH][hapmap]
rs2290067	0.94[GIH][hapmap]
rs2334230	0.94[GIH][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap]
rs2439222	0.92[GIH][hapmap]
rs2454673	0.94[GIH][hapmap];0.88[TSI][hapmap]
rs2454682	0.92[GIH][hapmap]
rs2454685	0.92[GIH][hapmap]
rs2470867	0.94[GIH][hapmap];0.84[TSI][hapmap]
rs2470869	0.92[GIH][hapmap]
rs2470885	0.94[GIH][hapmap];0.86[TSI][hapmap]
rs3755574	0.94[GIH][hapmap]
rs3755576	0.97[GIH][hapmap];0.89[TSI][hapmap]
rs4425200	0.94[GIH][hapmap]
rs4425201	0.83[ASW][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap]
rs6785935	0.97[GIH][hapmap];0.86[TSI][hapmap]
rs704585	0.97[GIH][hapmap];0.82[TSI][hapmap]
rs7431448	1.00[GIH][hapmap];0.86[TSI][hapmap]
rs828609	0.97[GIH][hapmap];0.82[TSI][hapmap]
rs9843214	0.82[ASW][hapmap];0.97[GIH][hapmap];0.86[TSI][hapmap]
rs9883537	0.94[GIH][hapmap]
rs999147	0.94[GIH][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
rs1440153	ST3GAL6	cis	parietal	SCAN
rs1440153	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL
rs1440153	ZBTB11	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98477000-98490200	Enhancers	Fetal Heart	heart
2	chr3:98478800-98515200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:98482200-98495800	Weak transcription	Dnd41	blood
4	chr3:98482400-98496000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:98482600-98494600	Weak transcription	Aorta	Aorta
6	chr3:98482600-98501800	Weak transcription	Fetal Stomach	stomach
7	chr3:98482800-98497400	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:98483000-98497400	Weak transcription	Spleen	Spleen
9	chr3:98483000-98517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:98483200-98518000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:98483600-98495200	Weak transcription	Fetal Thymus	thymus
12	chr3:98483600-98513600	Weak transcription	Brain Germinal Matrix	brain
13	chr3:98483800-98496400	Weak transcription	Fetal Lung	lung
14	chr3:98483800-98515000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:98484000-98498000	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr3:98484000-98514000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:98484200-98515200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:98484800-98529800	Weak transcription	Primary B cells from cord blood	blood
19	chr3:98485000-98496200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:98485400-98491600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr3:98487200-98489800	Genic enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:98487600-98490000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:98487600-98490800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:98487800-98489800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr3:98487800-98489800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:98487800-98490400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:98488000-98490800	Weak transcription	Liver	Liver
28	chr3:98488200-98489800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:98488200-98489800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr3:98488200-98496800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:98488600-98496200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:98488600-98497200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:98488600-98497200	Weak transcription	Fetal Kidney	kidney
34	chr3:98488800-98490000	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr3:98488800-98490200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:98489000-98489800	Enhancers	Placenta	Placenta
37	chr3:98489000-98489800	Enhancers	Thymus	Thymus
38	chr3:98489000-98490200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr3:98489200-98489800	Enhancers	Adipose Nuclei	Adipose
40	chr3:98489200-98489800	Enhancers	Pancreas	Pancrea
41	chr3:98489200-98489800	Enhancers	Psoas Muscle	Psoas
42	chr3:98489200-98489800	Enhancers	Right Ventricle	heart
43	chr3:98489200-98493200	Strong transcription	HUVEC	blood vessel
44	chr3:98489400-98489800	Enhancers	Primary T cells fromperipheralblood	blood
45	chr3:98489400-98489800	Enhancers	Stomach Mucosa	stomach
46	chr3:98489400-98489800	Flanking Active TSS	GM12878-XiMat	blood
47	chr3:98489400-98490000	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr3:98489400-98490200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:98489400-98491200	Strong transcription	HepG2	liver
50	chr3:98489600-98489800	Flanking Active TSS	Brain Anterior Caudate	brain

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