Variant report

Variant	rs278370
Chromosome Location	chr3:98452187-98452188
allele	G/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	MAX	chr3:98450640-98452402	HepG2	liver:	n/a	chr3:98450774-98450787
2	POLR2A	chr3:98450947-98452937	GM15510	blood:	n/a	n/a
3	MTA3	chr3:98452065-98453516	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:98450943-98452948	NB4	blood:	n/a	n/a
5	CEBPB	chr3:98452044-98452412	HepG2	liver:	n/a	chr3:98452226-98452239 chr3:98452227-98452238 chr3:98452228-98452237 chr3:98452226-98452237
6	TAF1	chr3:98450992-98452266	ECC-1	luminal epithelium:	n/a	n/a
7	E2F6	chr3:98450924-98452675	H1-hESC	embryonic stem cell:	n/a	n/a
8	RAD21	chr3:98451742-98452229	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:98450955-98452317	H1-neurons	neurons:	n/a	n/a
10	MAX	chr3:98451013-98452267	H1-hESC	embryonic stem cell:	n/a	n/a
11	TAF1	chr3:98450982-98452267	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:98450780-98453122	GM12878	blood:	n/a	n/a
13	POLR2A	chr3:98450967-98452250	HepG2	liver:	n/a	n/a
14	CEBPB	chr3:98452119-98452277	HepG2	liver:	n/a	chr3:98452226-98452239 chr3:98452227-98452238 chr3:98452228-98452237 chr3:98452226-98452237
15	POLR2A	chr3:98450870-98452234	HUVEC	blood vessel:	n/a	n/a
16	CEBPB	chr3:98451999-98452468	ECC-1	luminal epithelium:	n/a	chr3:98452226-98452239 chr3:98452227-98452238 chr3:98452228-98452237 chr3:98452226-98452237
17	HEY1	chr3:98451820-98452439	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:98450944-98453010	GM18951	blood:	n/a	n/a
19	CEBPB	chr3:98452066-98452405	H1-hESC	embryonic stem cell:	n/a	chr3:98452226-98452239 chr3:98452227-98452238 chr3:98452228-98452237 chr3:98452226-98452237
20	REST	chr3:98450799-98452473	H1-neurons	neurons:	n/a	chr3:98452007-98452021 chr3:98450942-98450950 chr3:98451980-98451987
21	POLR2A	chr3:98450763-98453265	GM18505	blood:	n/a	n/a
22	MXI1	chr3:98451668-98453310	GM12878	blood:	n/a	n/a
23	CHD1	chr3:98450677-98453146	GM12878	blood:	n/a	n/a
24	CEBPB	chr3:98452008-98452434	MCF-7	breast:	n/a	chr3:98452226-98452239 chr3:98452227-98452238 chr3:98452228-98452237 chr3:98452226-98452237
25	NFATC1	chr3:98451555-98452235	GM12878	blood:	n/a	n/a
26	MAX	chr3:98450909-98452293	ECC-1	luminal epithelium:	n/a	n/a
27	CEBPB	chr3:98452187-98452302	K562	blood:	n/a	chr3:98452226-98452239 chr3:98452227-98452238 chr3:98452228-98452237 chr3:98452226-98452237
28	MXI1	chr3:98450348-98454808	SK-N-SH	brain:	n/a	n/a
29	MAX	chr3:98450654-98453162	HepG2	liver:	n/a	chr3:98450774-98450787
30	PML	chr3:98450666-98453312	GM12878	blood:	n/a	n/a
31	BHLHE40	chr3:98450607-98452299	GM12878	blood:	n/a	chr3:98450776-98450785 chr3:98450776-98450785 chr3:98450774-98450787 chr3:98450775-98450784 chr3:98450770-98450791
32	ZBTB7A	chr3:98450978-98452316	ECC-1	luminal epithelium:	n/a	n/a
33	TCF12	chr3:98451488-98452196	A549	lung:	n/a	n/a
34	CEBPB	chr3:98452081-98452433	A549	lung:	n/a	chr3:98452226-98452239 chr3:98452227-98452238 chr3:98452228-98452237 chr3:98452226-98452237
35	CEBPB	chr3:98452128-98452429	ECC-1	luminal epithelium:	n/a	chr3:98452226-98452239 chr3:98452227-98452238 chr3:98452228-98452237 chr3:98452226-98452237
36	YY1	chr3:98451074-98452288	HepG2	liver:	n/a	n/a
37	POLR2A	chr3:98450906-98452291	GM12892	blood:	n/a	n/a
38	POLR2A	chr3:98450924-98452970	GM12892	blood:	n/a	n/a
39	MAZ	chr3:98451903-98452948	GM12878	blood:	n/a	n/a
40	EGR1	chr3:98451818-98452263	ECC-1	luminal epithelium:	n/a	chr3:98451959-98451972 chr3:98452028-98452038 chr3:98452026-98452039 chr3:98452027-98452041 chr3:98452026-98452039 chr3:98452026-98452040 chr3:98452027-98452038
41	POLR2A	chr3:98450760-98452997	GM12878	blood:	n/a	n/a
42	CHD2	chr3:98451058-98452381	HepG2	liver:	n/a	n/a
43	EGR1	chr3:98451844-98452269	ECC-1	luminal epithelium:	n/a	chr3:98451959-98451972 chr3:98452028-98452038 chr3:98452026-98452039 chr3:98452027-98452041 chr3:98452026-98452039 chr3:98452026-98452040 chr3:98452027-98452038
44	POLR2A	chr3:98451062-98452460	H1-hESC	embryonic stem cell:	n/a	n/a
45	MAX	chr3:98450860-98452343	A549	lung:	n/a	n/a
46	MAX	chr3:98451950-98453342	GM12878	blood:	n/a	n/a
47	MAX	chr3:98451920-98452445	SK-N-SH	brain:	n/a	n/a
48	TAF1	chr3:98451024-98452208	HepG2	liver:	n/a	n/a
49	POLR2A	chr3:98450852-98453465	GM12878	blood:	n/a	n/a
50	STAT5A	chr3:98451941-98453015	GM12878	blood:	n/a	chr3:98452229-98452237

Variant related genes	Relation type
ST3GAL6-AS1	TF binding region
ST3GAL6	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs115931	0.89[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1530655	0.81[JPT][hapmap]
rs278363	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs278373	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap]
rs278374	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs3821358	0.81[JPT][hapmap]
rs828589	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs828593	0.82[AMR][1000 genomes]
rs828594	0.81[CEU][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes]
rs828595	0.88[CEU][hapmap];0.80[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs828596	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs828597	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs828598	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs828599	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs828602	0.86[AMR][1000 genomes]
rs828613	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs844159	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs844161	0.85[CEU][hapmap];0.86[AMR][1000 genomes]
rs865474	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs893831	0.81[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs893832	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1003922	chr3:98410967-98453602	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv536662	chr3:98410967-98453602	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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
6	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
7	nsv470783	chr3:98431225-98466222	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	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
rs278370	ST3GAL6-AS1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98450400-98453000	Active TSS	Brain Anterior Caudate	brain
2	chr3:98450600-98452600	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr3:98450600-98453000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:98450600-98453000	Active TSS	Skeletal Muscle Male	skeletal muscle
5	chr3:98450600-98453200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:98450600-98453200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:98450600-98453200	Active TSS	Fetal Brain Female	brain
8	chr3:98450600-98453400	Active TSS	Brain Angular Gyrus	brain
9	chr3:98450600-98453400	Active TSS	Brain Cingulate Gyrus	brain
10	chr3:98450600-98453400	Active TSS	Brain Substantia Nigra	brain
11	chr3:98450600-98453600	Active TSS	Thymus	Thymus
12	chr3:98450600-98453800	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr3:98450600-98454000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:98450600-98454200	Active TSS	Fetal Kidney	kidney
15	chr3:98450600-98455600	Active TSS	GM12878-XiMat	blood
16	chr3:98450800-98452200	Active TSS	A549	lung
17	chr3:98450800-98452400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:98450800-98452400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:98450800-98452600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:98450800-98452600	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
21	chr3:98450800-98452800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
22	chr3:98450800-98452800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:98450800-98452800	Active TSS	Brain Hippocampus Middle	brain
24	chr3:98450800-98452800	Active TSS	Fetal Lung	lung
25	chr3:98450800-98452800	Active TSS	Rectal Smooth Muscle	rectum
26	chr3:98450800-98453000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr3:98450800-98453000	Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr3:98450800-98453000	Active TSS	Placenta Amnion	Placenta Amnion
29	chr3:98450800-98453200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:98450800-98453200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:98450800-98453200	Active TSS	Aorta	Aorta
32	chr3:98450800-98453400	Active TSS	Psoas Muscle	Psoas
33	chr3:98450800-98453600	Active TSS	Left Ventricle	heart
34	chr3:98450800-98453800	Active TSS	Right Atrium	heart
35	chr3:98450800-98454000	Active TSS	Right Ventricle	heart
36	chr3:98451000-98452200	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr3:98451000-98452200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr3:98451000-98452200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
39	chr3:98451000-98452200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
40	chr3:98451000-98452200	Active TSS	Fetal Intestine Large	intestine
41	chr3:98451000-98452200	Active TSS	NHDF-Ad	bronchial
42	chr3:98451000-98452400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:98451000-98452400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:98451000-98452400	Active TSS	Cortex derived primary cultured neurospheres	brain
45	chr3:98451000-98452400	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:98451000-98452600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
47	chr3:98451000-98452600	Active TSS	NH-A	brain
48	chr3:98451000-98452600	Active TSS	NHLF	lung
49	chr3:98451000-98452800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr3:98451000-98452800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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