Variant report

Variant	rs3766382
Chromosome Location	chr1:161008803-161008804
allele	A/C/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	POLR2A	chr1:161008153-161009077	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:161007957-161009036	GM12878	blood:	n/a	n/a
3	GABPA	chr1:161008425-161009005	GM12878	blood:	n/a	n/a
4	EP300	chr1:161008698-161009057	GM12878	blood:	n/a	chr1:161009016-161009030 chr1:161008802-161008811
5	ELK1	chr1:161008531-161008988	GM12878	blood:	n/a	n/a
6	SIN3AK20	chr1:161007599-161009021	MCF-7	breast:	n/a	n/a
7	ZEB1	chr1:161008429-161008903	GM12878	blood:	n/a	chr1:161008813-161008824 chr1:161008530-161008537
8	HA-E2F1	chr1:161008205-161009059	MCF-7	breast:	n/a	chr1:161008803-161008813 chr1:161008799-161008808
9	EGR1	chr1:161007843-161009279	HCT-116	colon:	n/a	chr1:161008803-161008816 chr1:161008803-161008813 chr1:161008804-161008815 chr1:161008803-161008816 chr1:161008804-161008814 chr1:161008804-161008814 chr1:161008804-161008813 chr1:161008803-161008816 chr1:161008802-161008816 chr1:161008802-161008817 chr1:161008803-161008816
10	MAZ	chr1:161008337-161009018	GM12878	blood:	n/a	n/a
11	MAX	chr1:161008360-161009052	H1-hESC	embryonic stem cell:	n/a	n/a
12	NFATC1	chr1:161008263-161009032	GM12878	blood:	n/a	n/a
13	TAF1	chr1:161008403-161009059	H1-hESC	embryonic stem cell:	n/a	n/a
14	EGR1	chr1:161008552-161008931	GM12878	blood:	n/a	chr1:161008803-161008816 chr1:161008803-161008813 chr1:161008804-161008815 chr1:161008803-161008816 chr1:161008804-161008814 chr1:161008804-161008814 chr1:161008804-161008813 chr1:161008803-161008816 chr1:161008802-161008816 chr1:161008802-161008817 chr1:161008803-161008816
15	CTCF	chr1:161008768-161008864	Lung_OC	lung:	n/a	n/a
16	GABPA	chr1:161008513-161008973	H1-hESC	embryonic stem cell:	n/a	n/a
17	NFATC1	chr1:161008346-161008953	GM12878	blood:	n/a	n/a
18	YY1	chr1:161008296-161009030	GM12892	blood:	n/a	chr1:161008802-161008816 chr1:161008788-161008802 chr1:161008802-161008811 chr1:161008799-161008808
19	GABPA	chr1:161008503-161009061	HL-60	blood:	n/a	n/a
20	POLR2A	chr1:161008284-161009056	GM12878	blood:	n/a	n/a
21	MAX	chr1:161008311-161008937	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr1:161008342-161008977	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr1:161007917-161009059	GM12891	blood:	n/a	n/a
24	TEAD4	chr1:161007992-161009049	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr1:161008050-161009032	ECC-1	luminal epithelium:	n/a	n/a
26	RUNX3	chr1:161008339-161009099	GM12878	blood:	n/a	n/a
27	POLR2A	chr1:161008326-161009033	GM12892	blood:	n/a	n/a
28	YY1	chr1:161008434-161008854	K562	blood:	n/a	chr1:161008802-161008816 chr1:161008788-161008802 chr1:161008802-161008811 chr1:161008799-161008808
29	STAT5A	chr1:161007852-161009029	GM12878	blood:	n/a	chr1:161008902-161008925
30	BCLAF1	chr1:161008416-161009012	GM12878	blood:	n/a	chr1:161008801-161008810
31	PAX5	chr1:161008558-161008886	GM12878	blood:	n/a	n/a
32	TCF12	chr1:161008703-161008900	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr1:161008326-161008946	HUVEC	blood vessel:	n/a	n/a
34	YY1	chr1:161008449-161008857	GM12891	blood:	n/a	chr1:161008802-161008816 chr1:161008788-161008802 chr1:161008802-161008811 chr1:161008799-161008808
35	NFIC	chr1:161008452-161009000	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:161008413-161008938	MCF10A-Er-Src	breast:	n/a	n/a
37	ZEB1	chr1:161008193-161009027	GM12878	blood:	n/a	chr1:161008813-161008824 chr1:161008530-161008537
38	POLR2A	chr1:161008429-161008984	H1-hESC	embryonic stem cell:	n/a	n/a
39	SIN3AK20	chr1:161007947-161008997	MCF-7	breast:	n/a	n/a
40	POU2F2	chr1:161008228-161009020	GM12891	blood:	n/a	chr1:161008804-161008816 chr1:161008807-161008819
41	POLR2A	chr1:161008039-161009078	H1-hESC	embryonic stem cell:	n/a	n/a
42	ELF1	chr1:161008302-161009015	GM12878	blood:	n/a	chr1:161008641-161008653
43	EBF1	chr1:161008555-161008907	GM12878	blood:	n/a	n/a
44	MAX	chr1:161007953-161009085	ECC-1	luminal epithelium:	n/a	n/a
45	POLR2A	chr1:161007856-161009025	GM12878	blood:	n/a	n/a
46	FOXM1	chr1:161008181-161009147	GM12878	blood:	n/a	n/a
47	PML	chr1:161008466-161008902	GM12878	blood:	n/a	n/a
48	POLR2A	chr1:161008322-161009024	HUVEC	blood vessel:	n/a	n/a
49	MXI1	chr1:161007229-161009255	SK-N-SH	brain:	n/a	n/a
50	MXI1	chr1:161008502-161009034	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:161006227..161009098-chr1:161086419..161089402,2	MCF-7	breast:
2	chr1:161007165..161010190-chr1:161058502..161060475,3	MCF-7	breast:
3	chr1:161007047..161009717-chr1:161100084..161102311,2	K562	blood:
4	chr1:160989087..160991942-chr1:161007144..161014242,6	K562	blood:
5	chr1:161007801..161009697-chr1:161067796..161070375,2	K562	blood:
6	chr1:161006354..161009878-chr1:161042497..161045575,4	MCF-7	breast:
7	chr1:160988819..160994033-chr1:161005548..161011188,8	MCF-7	breast:
8	chr1:161007064..161010778-chr1:161101040..161104167,3	MCF-7	breast:
9	chr1:160990711..160991608-chr1:161008481..161009243,2	MCF-7	breast:
10	chr1:160989495..160995605-chr1:161004888..161010340,15	MCF-7	breast:
11	chr1:161006846..161009787-chr1:161123441..161125743,2	MCF-7	breast:
12	chr1:160988071..160992174-chr1:161007125..161014242,7	K562	blood:
13	chr1:161005808..161012985-chr1:161064732..161070101,9	MCF-7	breast:

Variant related genes	Relation type
TSTD1	TF binding region
ENSG00000270149	TF binding region
ENSG00000143222	Chromatin interaction
ENSG00000158796	Chromatin interaction
ENSG00000158793	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000143256	Chromatin interaction
ENSG00000143217	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12036299	0.81[EUR][1000 genomes]
rs1556259	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1556260	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1974140	0.90[EUR][1000 genomes]
rs2073653	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3766383	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57839241	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58318788	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs58974723	0.87[EUR][1000 genomes]
rs6427572	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6427573	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6660240	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6686076	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6701822	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7516231	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv947201	chr1:161006051-161013276	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv548059	chr1:161007326-161010791	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3766382	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs3766382	ENSG00000215845	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161004000-161009200	Weak transcription	Hela-S3	cervix
2	chr1:161005000-161009400	Weak transcription	K562	blood
3	chr1:161007000-161009200	Weak transcription	NHDF-Ad	bronchial
4	chr1:161007000-161013400	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr1:161007200-161009000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr1:161007400-161009000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr1:161007400-161009200	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr1:161007400-161009200	Active TSS	Rectal Smooth Muscle	rectum
9	chr1:161007400-161013400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:161007400-161013400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:161007400-161013400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:161007400-161013400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:161007600-161009000	Active TSS	ES-I3 Cell Line	embryonic stem cell
14	chr1:161007600-161009000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
15	chr1:161007600-161009000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:161007600-161009000	Active TSS	Colon Smooth Muscle	Colon
17	chr1:161007600-161009200	Flanking Active TSS	Dnd41	blood
18	chr1:161007600-161009200	Weak transcription	HepG2	liver
19	chr1:161007600-161009400	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
20	chr1:161007600-161013400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr1:161007800-161009000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:161007800-161009000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:161007800-161009000	Active TSS	Brain Hippocampus Middle	brain
24	chr1:161007800-161009000	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr1:161007800-161009000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr1:161007800-161009000	Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr1:161007800-161009000	Transcr. at gene 5' and 3'	Placenta	Placenta
28	chr1:161007800-161009000	Active TSS	HSMMtube	muscle
29	chr1:161007800-161009200	Active TSS	H9 Cell Line	embryonic stem cell
30	chr1:161007800-161009200	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr1:161007800-161009200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr1:161007800-161009200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
33	chr1:161007800-161009200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
34	chr1:161007800-161009400	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr1:161008000-161009000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:161008000-161009000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr1:161008000-161009000	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr1:161008000-161009000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr1:161008000-161009000	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
40	chr1:161008000-161009000	Active TSS	Brain Anterior Caudate	brain
41	chr1:161008000-161009000	Active TSS	Fetal Kidney	kidney
42	chr1:161008000-161009000	Flanking Active TSS	Fetal Thymus	thymus
43	chr1:161008000-161009000	Active TSS	Ovary	ovary
44	chr1:161008000-161009000	Active TSS	Placenta Amnion	Placenta Amnion
45	chr1:161008000-161009000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
46	chr1:161008000-161009000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr1:161008000-161009200	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr1:161008000-161009200	Flanking Active TSS	Liver	Liver
49	chr1:161008000-161013200	Strong transcription	A549	lung
50	chr1:161008000-161013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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