Variant report

Variant	rs3813309
Chromosome Location	chr5:118690998-118690999
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:80)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:80 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:118688526-118696061	GM12878	blood:	n/a	n/a
2	HA-E2F1	chr5:118690803-118691952	MCF-7	breast:	n/a	chr5:118691641-118691653 chr5:118690878-118690887
3	POLR2A	chr5:118690622-118693443	GM19193	blood:	n/a	n/a
4	CEBPB	chr5:118690985-118691271	HepG2	liver:	n/a	n/a
5	RELA	chr5:118690557-118694108	GM12891	blood:	n/a	n/a
6	TBP	chr5:118689422-118692594	GM12878	blood:	n/a	n/a
7	POLR2A	chr5:118690900-118691047	H1-hESC	embryonic stem cell:	n/a	n/a
8	MYC	chr5:118690875-118691156	H1-hESC	embryonic stem cell:	n/a	n/a
9	TAF1	chr5:118690920-118691168	GM12892	blood:	n/a	n/a
10	MAZ	chr5:118690555-118692953	IMR90	lung:	n/a	chr5:118692461-118692472
11	SMC3	chr5:118690998-118691157	Hela-S3	cervix:	n/a	n/a
12	PML	chr5:118690397-118693186	GM12878	blood:	n/a	chr5:118692075-118692083
13	POU2F2	chr5:118690744-118691203	GM12891	blood:	n/a	n/a
14	POLR2A	chr5:118690288-118692832	GM12892	blood:	n/a	n/a
15	NFATC1	chr5:118690799-118691972	GM12878	blood:	n/a	n/a
16	POLR2A	chr5:118690266-118692633	GM12892	blood:	n/a	n/a
17	FOS	chr5:118690908-118691275	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr5:118690639-118692349	GM12878	blood:	n/a	n/a
19	POLR2A	chr5:118690511-118692628	GM12892	blood:	n/a	n/a
20	TCF7L2	chr5:118690919-118691287	Hela-S3	cervix:	n/a	n/a
21	WRNIP1	chr5:118690665-118691031	GM12878	blood:	n/a	n/a
22	GTF2F1	chr5:118690917-118691067	H1-hESC	embryonic stem cell:	n/a	n/a
23	RELA	chr5:118690644-118693165	GM10847	blood:	n/a	n/a
24	TCF7L2	chr5:118690889-118691452	MCF-7	breast:	n/a	n/a
25	CHD1	chr5:118688941-118694425	GM12878	blood:	n/a	n/a
26	JUND	chr5:118690972-118691901	H1-hESC	embryonic stem cell:	n/a	n/a
27	FOXM1	chr5:118690381-118691171	GM12878	blood:	n/a	n/a
28	POLR2A	chr5:118690468-118692879	GM18526	blood:	n/a	n/a
29	SMARCC1	chr5:118690685-118691660	Hela-S3	cervix:	n/a	n/a
30	MYC	chr5:118690910-118691338	MCF10A-Er-Src	breast:	n/a	n/a
31	POLR2A	chr5:118689028-118697007	GM18505	blood:	n/a	n/a
32	POLR2A	chr5:118689433-118694184	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:118688841-118700411	GM12891	blood:	n/a	n/a
34	POLR2A	chr5:118690578-118692276	GM12891	blood:	n/a	n/a
35	POLR2A	chr5:118690529-118692929	GM12878	blood:	n/a	n/a
36	HDAC2	chr5:118690779-118691264	MCF-7	breast:	n/a	n/a
37	POLR2A	chr5:118690750-118691213	GM12891	blood:	n/a	n/a
38	POLR2A	chr5:118689446-118694162	GM19099	blood:	n/a	n/a
39	POLR2A	chr5:118690538-118691990	GM12892	blood:	n/a	n/a
40	FOS	chr5:118690851-118691235	MCF10A-Er-Src	breast:	n/a	n/a
41	FOXM1	chr5:118690494-118692880	GM12878	blood:	n/a	n/a
42	BCLAF1	chr5:118690659-118691201	GM12878	blood:	n/a	n/a
43	POLR2A	chr5:118689533-118692735	GM18951	blood:	n/a	n/a
44	SIN3A	chr5:118690977-118692192	H1-hESC	embryonic stem cell:	n/a	chr5:118691638-118691649
45	CTBP2	chr5:118690783-118692169	H1-hESC	embryonic stem cell:	n/a	n/a
46	EBF1	chr5:118690736-118692045	GM12878	blood:	n/a	n/a
47	POLR2A	chr5:118690931-118691128	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr5:118690744-118692293	H1-hESC	embryonic stem cell:	n/a	n/a
49	ZNF143	chr5:118690625-118691127	H1-hESC	embryonic stem cell:	n/a	n/a
50	STAT3	chr5:118690912-118691245	MCF10A-Er-Src	breast:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:118690955-118691005	HEK293	kidney:	embryo
2	chr5:118690955-118691005	ECC-1	luminal epithelium:	n/a
3	chr5:118690955-118691005	PANC-1	pancreas:	n/a
4	chr5:118690955-118691005	ovcar-3	ovarian:	n/a
5	chr5:118690955-118691005	NT2-D1	testis:	n/a
6	chr5:118690955-118691005	HIPEpiC	eye:	n/a
7	chr5:118690955-118691005	HCF	heart:	n/a
8	chr5:118690955-118691005	GM12891	blood:	n/a
9	chr5:118690955-118691005	A549	lung:	n/a
10	chr5:118690955-118691005	Jurkat	blood:	n/a
11	chr5:118690955-118691005	BE2_C	brain:	n/a
12	chr5:118690955-118691005	Hepatocyte	liver:	n/a
13	chr5:118690955-118691005	SAEC	small airway:	n/a
14	chr5:118690955-118691005	HCM	heart:	n/a
15	chr5:118690955-118691005	Caco-2	colon:	n/a
16	chr5:118690955-118691005	SK-N-MC	brain:	n/a
17	chr5:118690955-118691005	AG10803	skin:	n/a
18	chr5:118690955-118691005	HRCEpiC	kidney:	n/a
19	chr5:118690955-118691005	GM12892	blood:	n/a
20	chr5:118690955-118691005	H1-hESC	embryonic stem cell:	embryo
21	chr5:118690955-118691005	HCT-116	colon:	n/a
22	chr5:118690955-118691005	AG09319	gingival:	n/a
23	chr5:118690955-118691005	Hela-S3	cervix:	n/a
24	chr5:118690955-118691005	HUVEC	blood vessel:	n/a
25	chr5:118690955-118691005	PrEC	prostate:	n/a
26	chr5:118690955-118691005	MCF10A-Er-Src	breast:	n/a
27	chr5:118690955-118691005	SK-N-SH	brain:	n/a
28	chr5:118690955-118691005	PFSK-1	brain:	n/a
29	chr5:118690955-118691005	HCPEpiC	choroid plexus:	n/a
30	chr5:118690955-118691005	K562	blood:	n/a
31	chr5:118690955-118691005	ProgFib	skin:	n/a
32	chr5:118690955-118691005	GM19239	blood:	n/a
33	chr5:118690955-118691005	HEEpiC	esophagus:	n/a
34	chr5:118690955-118691005	HAEpiC	amniotic membrane:	n/a
35	chr5:118690955-118691005	NHDF-neo	bronchial:	n/a
36	chr5:118690955-118691005	GM06990	blood:	n/a
37	chr5:118690955-118691005	IMR90	lung:	fetal
38	chr5:118690955-118691005	HL-60	blood:	n/a
39	chr5:118690955-118691005	HepG2	liver:	n/a
40	chr5:118690955-118691005	NHBE	bronchial:	n/a
41	chr5:118690955-118691005	T-47D	breast:	n/a
42	chr5:118690955-118691005	MCF-7	breast:	n/a
43	chr5:118690955-118691005	SK-N-SH_RA	brain:	n/a
44	chr5:118690955-118691005	U87	brain:	n/a
45	chr5:118690955-118691005	AG09309	skin:	n/a
46	chr5:118690955-118691005	CMK	blood:	n/a
47	chr5:118690955-118691005	HMEC	breast:	n/a
48	chr5:118690955-118691005	HPAEpiC	pulmonary alveolar:	n/a
49	chr5:118690955-118691005	NH-A	brain:	n/a
50	chr5:118690955-118691005	HNPCEpiC	eye:	n/a

No data

Variant related genes	Relation type
TNFAIP8	TF binding region
TNFAIP8	CpG island

Extended variants
information (count: 28 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10077888	0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap]
rs10478422	0.80[JPT][hapmap]
rs1155268	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1490756	1.00[LWK][hapmap]
rs1509141	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509142	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509144	0.84[JPT][hapmap]
rs1848554	0.90[JPT][hapmap]
rs192225	1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs250298	0.81[CHB][hapmap]
rs250299	0.83[CHB][hapmap]
rs250302	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs250303	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs250304	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs257969	1.00[LWK][hapmap]
rs257973	1.00[LWK][hapmap]
rs32652	0.91[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs32654	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3797368	1.00[LWK][hapmap]
rs457106	1.00[LWK][hapmap]
rs4895369	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6595186	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6874848	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7721752	0.80[JPT][hapmap]
rs924623	0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869828	chr5:118610548-118691190	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv599565	chr5:118661882-118691888	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv882775	chr5:118669094-118691888	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118670800-118691000	Weak transcription	Aorta	Aorta
2	chr5:118671200-118695400	Weak transcription	A549	lung
3	chr5:118676800-118691400	Weak transcription	Lung	lung
4	chr5:118680800-118691000	Weak transcription	HSMMtube	muscle
5	chr5:118682600-118693600	Weak transcription	Dnd41	blood
6	chr5:118684000-118691000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:118684000-118691000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr5:118684000-118692800	Weak transcription	K562	blood
9	chr5:118684200-118691000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr5:118685000-118691000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr5:118687800-118691000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr5:118687800-118691000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr5:118688000-118691000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr5:118688600-118691200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:118688800-118691000	Enhancers	Adipose Nuclei	Adipose
16	chr5:118688800-118691400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:118689000-118691000	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr5:118689000-118691000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:118689000-118691000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:118689000-118691000	Enhancers	Fetal Stomach	stomach
21	chr5:118689000-118691200	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr5:118689000-118691200	Enhancers	Placenta	Placenta
23	chr5:118689000-118691200	Enhancers	NHDF-Ad	bronchial
24	chr5:118689000-118691400	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr5:118689200-118691000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr5:118689200-118691200	Enhancers	Fetal Heart	heart
27	chr5:118689400-118691000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr5:118689400-118691200	Enhancers	Fetal Thymus	thymus
29	chr5:118689400-118691400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr5:118689600-118691000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:118689600-118691200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr5:118689600-118692000	Flanking Active TSS	Primary B cells from cord blood	blood
33	chr5:118689800-118691000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
34	chr5:118689800-118691000	Enhancers	Primary hematopoietic stem cells	blood
35	chr5:118689800-118691000	Enhancers	Colon Smooth Muscle	Colon
36	chr5:118689800-118691000	Weak transcription	Spleen	Spleen
37	chr5:118689800-118691200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr5:118689800-118691200	Enhancers	Fetal Lung	lung
39	chr5:118690000-118691000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr5:118690000-118691000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:118690000-118691000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr5:118690000-118691000	Enhancers	Duodenum Mucosa	Duodenum
43	chr5:118690000-118691200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr5:118690000-118691400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr5:118690000-118691600	Weak transcription	Gastric	stomach
46	chr5:118690200-118691000	Active TSS	Rectal Mucosa Donor 29	rectum
47	chr5:118690400-118691400	Enhancers	Stomach Mucosa	stomach
48	chr5:118690400-118691400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr5:118690400-118692600	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr5:118690600-118691000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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