Variant report

Variant	rs278372
Chromosome Location	chr3:98453010-98453011
allele	A/C
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	SIN3A	chr3:98452544-98453048	GM12878	blood:	n/a	n/a
2	MTA3	chr3:98452065-98453516	GM12878	blood:	n/a	n/a
3	STAT1	chr3:98452732-98453085	GM12878	blood:	n/a	n/a
4	EBF1	chr3:98452663-98453023	GM12878	blood:	n/a	n/a
5	RUNX3	chr3:98452197-98453526	GM12878	blood:	n/a	chr3:98452878-98452893
6	POLR2A	chr3:98450780-98453122	GM12878	blood:	n/a	n/a
7	BHLHE40	chr3:98452642-98453330	GM12878	blood:	n/a	n/a
8	BCLAF1	chr3:98452265-98453111	GM12878	blood:	n/a	chr3:98452505-98452518
9	NR2C2	chr3:98452704-98453099	GM12878	blood:	n/a	chr3:98452905-98452918
10	POLR2A	chr3:98450944-98453010	GM18951	blood:	n/a	n/a
11	HNF4A	chr3:98452654-98453078	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
12	MYBL2	chr3:98452604-98453212	HepG2	liver:	n/a	n/a
13	RUNX3	chr3:98452578-98453159	GM12878	blood:	n/a	chr3:98452878-98452893
14	POLR2A	chr3:98452645-98453114	HepG2	liver:	n/a	n/a
15	STAT3	chr3:98452680-98453232	GM12878	blood:	n/a	n/a
16	POLR2A	chr3:98450763-98453265	GM18505	blood:	n/a	n/a
17	MXI1	chr3:98451668-98453310	GM12878	blood:	n/a	n/a
18	CHD1	chr3:98450677-98453146	GM12878	blood:	n/a	n/a
19	FOXA2	chr3:98452650-98453178	HepG2	liver:	n/a	n/a
20	CTCF	chr3:98452960-98453110	HRPEpiC	eye:	n/a	n/a
21	MXI1	chr3:98450348-98454808	SK-N-SH	brain:	n/a	n/a
22	MAX	chr3:98450654-98453162	HepG2	liver:	n/a	chr3:98450774-98450787
23	POLR2A	chr3:98452512-98453084	GM12892	blood:	n/a	n/a
24	PML	chr3:98450666-98453312	GM12878	blood:	n/a	n/a
25	BHLHE40	chr3:98452700-98453327	HepG2	liver:	n/a	n/a
26	MAX	chr3:98452701-98453036	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:98452545-98453069	GM12891	blood:	n/a	n/a
28	POLR2A	chr3:98452591-98453093	HepG2	liver:	n/a	n/a
29	MYC	chr3:98452651-98453101	HepG2	liver:	n/a	n/a
30	TBP	chr3:98452350-98453012	GM12878	blood:	n/a	n/a
31	MAX	chr3:98451950-98453342	GM12878	blood:	n/a	n/a
32	HEY1	chr3:98452525-98453092	HepG2	liver:	n/a	n/a
33	POLR2A	chr3:98450852-98453465	GM12878	blood:	n/a	n/a
34	STAT5A	chr3:98451941-98453015	GM12878	blood:	n/a	chr3:98452229-98452237
35	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
36	POLR2A	chr3:98452664-98453061	HepG2	liver:	n/a	n/a
37	RCOR1	chr3:98452610-98453076	GM12878	blood:	n/a	n/a
38	MXI1	chr3:98452621-98453141	HepG2	liver:	n/a	n/a
39	MAX	chr3:98452710-98453046	H1-hESC	embryonic stem cell:	n/a	n/a
40	EP300	chr3:98452432-98453012	GM12878	blood:	n/a	n/a
41	MAX	chr3:98452667-98453093	H1-hESC	embryonic stem cell:	n/a	n/a
42	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
43	ATF2	chr3:98452576-98453067	GM12878	blood:	n/a	n/a
44	MAX	chr3:98450665-98453243	NB4	blood:	n/a	chr3:98450774-98450787
45	MYC	chr3:98450805-98453212	NB4	blood:	n/a	n/a
46	POLR2A	chr3:98450939-98453036	GM12892	blood:	n/a	n/a
47	HNF4A	chr3:98452743-98453082	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
48	NFIC	chr3:98452009-98453500	GM12878	blood:	n/a	n/a
49	MAX	chr3:98452614-98453116	H1-hESC	embryonic stem cell:	n/a	n/a
50	MTA3	chr3:98451645-98453159	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ST3GAL6-AS1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1666291	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1666310	0.92[EUR][1000 genomes]
rs278364	0.83[ASN][1000 genomes]
rs278371	0.93[ASN][1000 genomes]
rs6792234	0.81[EUR][1000 genomes]
rs704580	0.93[EUR][1000 genomes]
rs828585	0.88[EUR][1000 genomes]
rs828587	0.88[EUR][1000 genomes]
rs828600	0.82[AMR][1000 genomes];0.95[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

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98450600-98453200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:98450600-98453200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:98450600-98453200	Active TSS	Fetal Brain Female	brain
4	chr3:98450600-98453400	Active TSS	Brain Angular Gyrus	brain
5	chr3:98450600-98453400	Active TSS	Brain Cingulate Gyrus	brain
6	chr3:98450600-98453400	Active TSS	Brain Substantia Nigra	brain
7	chr3:98450600-98453600	Active TSS	Thymus	Thymus
8	chr3:98450600-98453800	Active TSS	Pancreatic Islets	Pancreatic Islet
9	chr3:98450600-98454000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:98450600-98454200	Active TSS	Fetal Kidney	kidney
11	chr3:98450600-98455600	Active TSS	GM12878-XiMat	blood
12	chr3:98450800-98453200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:98450800-98453200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:98450800-98453200	Active TSS	Aorta	Aorta
15	chr3:98450800-98453400	Active TSS	Psoas Muscle	Psoas
16	chr3:98450800-98453600	Active TSS	Left Ventricle	heart
17	chr3:98450800-98453800	Active TSS	Right Atrium	heart
18	chr3:98450800-98454000	Active TSS	Right Ventricle	heart
19	chr3:98451000-98453200	Active TSS	Colon Smooth Muscle	Colon
20	chr3:98451000-98453200	Active TSS	Lung	lung
21	chr3:98451000-98453200	Active TSS	Ovary	ovary
22	chr3:98451200-98453200	Active TSS	Muscle Satellite Cultured Cells	--
23	chr3:98451200-98453800	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr3:98451400-98453400	Active TSS	Fetal Thymus	thymus
25	chr3:98452000-98453200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:98452000-98453200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
27	chr3:98452000-98453400	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr3:98452000-98453600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:98452200-98453200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:98452200-98453200	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr3:98452200-98453200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:98452200-98453200	Active TSS	Fetal Heart	heart
33	chr3:98452200-98453200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
34	chr3:98452200-98453400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:98452200-98453400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr3:98452200-98453400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
37	chr3:98452200-98453400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr3:98452200-98453400	Flanking Active TSS	Dnd41	blood
39	chr3:98452200-98453400	Flanking Bivalent TSS/Enh	Osteobl	bone
40	chr3:98452200-98453600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
41	chr3:98452200-98453600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:98452200-98455000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr3:98452400-98453200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:98452400-98453400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
45	chr3:98452400-98454000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr3:98452600-98453200	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr3:98452600-98453400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr3:98452600-98453400	Flanking Active TSS	Fetal Brain Male	brain
49	chr3:98452600-98453400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
50	chr3:98452600-98453400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links