Variant report

Variant	rs1440149
Chromosome Location	chr3:98452653-98452654
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	ARID3A	chr3:98452261-98452798	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:98450947-98452937	GM15510	blood:	n/a	n/a
3	SIN3A	chr3:98452544-98453048	GM12878	blood:	n/a	n/a
4	MTA3	chr3:98452065-98453516	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:98450943-98452948	NB4	blood:	n/a	n/a
6	E2F6	chr3:98450924-98452675	H1-hESC	embryonic stem cell:	n/a	n/a
7	RUNX3	chr3:98452197-98453526	GM12878	blood:	n/a	chr3:98452878-98452893
8	POLR2A	chr3:98450780-98453122	GM12878	blood:	n/a	n/a
9	TBL1XR1	chr3:98452498-98453006	GM12878	blood:	n/a	n/a
10	BHLHE40	chr3:98452642-98453330	GM12878	blood:	n/a	n/a
11	BCLAF1	chr3:98452265-98453111	GM12878	blood:	n/a	chr3:98452505-98452518
12	SIN3AK20	chr3:98452356-98452917	SK-N-SH	brain:	n/a	n/a
13	POLR2A	chr3:98450944-98453010	GM18951	blood:	n/a	n/a
14	POLR2A	chr3:98452651-98452994	HepG2	liver:	n/a	n/a
15	MYBL2	chr3:98452604-98453212	HepG2	liver:	n/a	n/a
16	RUNX3	chr3:98452578-98453159	GM12878	blood:	n/a	chr3:98452878-98452893
17	POLR2A	chr3:98452645-98453114	HepG2	liver:	n/a	n/a
18	POLR2A	chr3:98450763-98453265	GM18505	blood:	n/a	n/a
19	MXI1	chr3:98451668-98453310	GM12878	blood:	n/a	n/a
20	CHD1	chr3:98450677-98453146	GM12878	blood:	n/a	n/a
21	FOXA2	chr3:98452650-98453178	HepG2	liver:	n/a	n/a
22	MXI1	chr3:98450348-98454808	SK-N-SH	brain:	n/a	n/a
23	MAX	chr3:98450654-98453162	HepG2	liver:	n/a	chr3:98450774-98450787
24	POLR2A	chr3:98452512-98453084	GM12892	blood:	n/a	n/a
25	PML	chr3:98450666-98453312	GM12878	blood:	n/a	n/a
26	BCL3	chr3:98452563-98452971	GM12878	blood:	n/a	n/a
27	TCF12	chr3:98452630-98452997	GM12878	blood:	n/a	chr3:98452815-98452825
28	POLR2A	chr3:98452545-98453069	GM12891	blood:	n/a	n/a
29	POLR2A	chr3:98452591-98453093	HepG2	liver:	n/a	n/a
30	MYC	chr3:98452651-98453101	HepG2	liver:	n/a	n/a
31	TBP	chr3:98452350-98453012	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:98450924-98452970	GM12892	blood:	n/a	n/a
33	MAZ	chr3:98451903-98452948	GM12878	blood:	n/a	n/a
34	POLR2A	chr3:98450760-98452997	GM12878	blood:	n/a	n/a
35	MAX	chr3:98451950-98453342	GM12878	blood:	n/a	n/a
36	HEY1	chr3:98452525-98453092	HepG2	liver:	n/a	n/a
37	SMC3	chr3:98452481-98452998	GM12878	blood:	n/a	chr3:98452876-98452884 chr3:98452674-98452684
38	POLR2A	chr3:98450852-98453465	GM12878	blood:	n/a	n/a
39	STAT5A	chr3:98451941-98453015	GM12878	blood:	n/a	chr3:98452229-98452237
40	HNF4A	chr3:98452562-98453067	HepG2	liver:	n/a	chr3:98452900-98452922 chr3:98452879-98452894 chr3:98452905-98452917 chr3:98452904-98452918 chr3:98452903-98452918 chr3:98452905-98452917 chr3:98452904-98452918 chr3:98452904-98452919 chr3:98452903-98452918 chr3:98452903-98452918 chr3:98452904-98452918 chr3:98452904-98452916 chr3:98452905-98452917 chr3:98452903-98452918 chr3:98452902-98452920 chr3:98452904-98452917 chr3:98452905-98452918 chr3:98452905-98452918 chr3:98452903-98452918 chr3:98452905-98452918
41	RCOR1	chr3:98452610-98453076	GM12878	blood:	n/a	n/a
42	MXI1	chr3:98452621-98453141	HepG2	liver:	n/a	n/a
43	EP300	chr3:98452432-98453012	GM12878	blood:	n/a	n/a
44	HNF4G	chr3:98452616-98453101	HepG2	liver:	n/a	chr3:98452900-98452922 chr3:98452905-98452917 chr3:98452904-98452918 chr3:98452903-98452918 chr3:98452905-98452917 chr3:98452904-98452918 chr3:98452904-98452919 chr3:98452903-98452918 chr3:98452903-98452918 chr3:98452904-98452918 chr3:98452904-98452916 chr3:98452905-98452917 chr3:98452903-98452918 chr3:98452902-98452920 chr3:98452904-98452917 chr3:98452905-98452918 chr3:98452905-98452918 chr3:98452905-98452918
45	ATF2	chr3:98452576-98453067	GM12878	blood:	n/a	n/a
46	MAX	chr3:98450665-98453243	NB4	blood:	n/a	chr3:98450774-98450787
47	MYC	chr3:98450805-98453212	NB4	blood:	n/a	n/a
48	POLR2A	chr3:98450939-98453036	GM12892	blood:	n/a	n/a
49	NFIC	chr3:98452009-98453500	GM12878	blood:	n/a	n/a
50	MAX	chr3:98452614-98453116	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ST3GAL6-AS1	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10470451	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11923134	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12494828	0.83[EUR][1000 genomes]
rs12496694	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13315676	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1440155	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1440158	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1530655	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1868217	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28553326	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28707457	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3755569	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3755570	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3772091	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3821358	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4638909	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56976804	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60464352	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62276459	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62278471	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62278472	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7611040	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7614161	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7620634	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7620636	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7628381	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7630887	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7631062	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7643537	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7649812	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7652790	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828593	0.85[ASN][1000 genomes]
rs828594	0.84[ASN][1000 genomes]
rs9858954	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9859711	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9879927	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][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
rs1440149	ST3GAL6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 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	chr3:98450600-98453000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:98450600-98453000	Active TSS	Skeletal Muscle Male	skeletal muscle
4	chr3:98450600-98453200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:98450600-98453200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:98450600-98453200	Active TSS	Fetal Brain Female	brain
7	chr3:98450600-98453400	Active TSS	Brain Angular Gyrus	brain
8	chr3:98450600-98453400	Active TSS	Brain Cingulate Gyrus	brain
9	chr3:98450600-98453400	Active TSS	Brain Substantia Nigra	brain
10	chr3:98450600-98453600	Active TSS	Thymus	Thymus
11	chr3:98450600-98453800	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr3:98450600-98454000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:98450600-98454200	Active TSS	Fetal Kidney	kidney
14	chr3:98450600-98455600	Active TSS	GM12878-XiMat	blood
15	chr3:98450800-98452800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:98450800-98452800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:98450800-98452800	Active TSS	Brain Hippocampus Middle	brain
18	chr3:98450800-98452800	Active TSS	Fetal Lung	lung
19	chr3:98450800-98452800	Active TSS	Rectal Smooth Muscle	rectum
20	chr3:98450800-98453000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:98450800-98453000	Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr3:98450800-98453000	Active TSS	Placenta Amnion	Placenta Amnion
23	chr3:98450800-98453200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr3:98450800-98453200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:98450800-98453200	Active TSS	Aorta	Aorta
26	chr3:98450800-98453400	Active TSS	Psoas Muscle	Psoas
27	chr3:98450800-98453600	Active TSS	Left Ventricle	heart
28	chr3:98450800-98453800	Active TSS	Right Atrium	heart
29	chr3:98450800-98454000	Active TSS	Right Ventricle	heart
30	chr3:98451000-98452800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr3:98451000-98452800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr3:98451000-98452800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:98451000-98452800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
34	chr3:98451000-98452800	Active TSS	Esophagus	oesophagus
35	chr3:98451000-98453000	Active TSS	Gastric	stomach
36	chr3:98451000-98453000	Active TSS	Pancreas	Pancrea
37	chr3:98451000-98453200	Active TSS	Colon Smooth Muscle	Colon
38	chr3:98451000-98453200	Active TSS	Lung	lung
39	chr3:98451000-98453200	Active TSS	Ovary	ovary
40	chr3:98451200-98452800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr3:98451200-98452800	Active TSS	Primary T cells from cord blood	blood
42	chr3:98451200-98452800	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
43	chr3:98451200-98452800	Bivalent/Poised TSS	Fetal Stomach	stomach
44	chr3:98451200-98452800	Active TSS	HMEC	breast
45	chr3:98451200-98452800	Active TSS	HUVEC	blood vessel
46	chr3:98451200-98453000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
47	chr3:98451200-98453000	Active TSS	Liver	Liver
48	chr3:98451200-98453000	Bivalent/Poised TSS	HepG2	liver
49	chr3:98451200-98453200	Active TSS	Muscle Satellite Cultured Cells	--
50	chr3:98451200-98453800	Active TSS	Brain Inferior Temporal Lobe	brain

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