Variant report

Variant	rs3813308
Chromosome Location	chr5:118690781-118690782
allele	C/G
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	chr5:118688526-118696061	GM12878	blood:	n/a	n/a
2	POLR2A	chr5:118690622-118693443	GM19193	blood:	n/a	n/a
3	RELA	chr5:118690557-118694108	GM12891	blood:	n/a	n/a
4	TBP	chr5:118689422-118692594	GM12878	blood:	n/a	n/a
5	MAZ	chr5:118690555-118692953	IMR90	lung:	n/a	chr5:118692461-118692472
6	PML	chr5:118690397-118693186	GM12878	blood:	n/a	chr5:118692075-118692083
7	POU2F2	chr5:118690744-118691203	GM12891	blood:	n/a	n/a
8	POLR2A	chr5:118690288-118692832	GM12892	blood:	n/a	n/a
9	EP300	chr5:118690670-118690870	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:118690266-118692633	GM12892	blood:	n/a	n/a
11	POLR2A	chr5:118690639-118692349	GM12878	blood:	n/a	n/a
12	POLR2A	chr5:118690511-118692628	GM12892	blood:	n/a	n/a
13	WRNIP1	chr5:118690665-118691031	GM12878	blood:	n/a	n/a
14	NFIC	chr5:118689581-118690843	GM12878	blood:	n/a	n/a
15	RELA	chr5:118690644-118693165	GM10847	blood:	n/a	n/a
16	CHD1	chr5:118688941-118694425	GM12878	blood:	n/a	n/a
17	FOXM1	chr5:118690381-118691171	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:118690468-118692879	GM18526	blood:	n/a	n/a
19	SMARCC1	chr5:118690685-118691660	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr5:118689028-118697007	GM18505	blood:	n/a	n/a
21	POLR2A	chr5:118689433-118694184	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:118688841-118700411	GM12891	blood:	n/a	n/a
23	POLR2A	chr5:118690578-118692276	GM12891	blood:	n/a	n/a
24	POLR2A	chr5:118690529-118692929	GM12878	blood:	n/a	n/a
25	HDAC2	chr5:118690779-118691264	MCF-7	breast:	n/a	n/a
26	POLR2A	chr5:118690750-118691213	GM12891	blood:	n/a	n/a
27	POLR2A	chr5:118689446-118694162	GM19099	blood:	n/a	n/a
28	POLR2A	chr5:118690538-118691990	GM12892	blood:	n/a	n/a
29	ZNF143	chr5:118690593-118690885	GM12878	blood:	n/a	n/a
30	FOXM1	chr5:118690494-118692880	GM12878	blood:	n/a	n/a
31	BCLAF1	chr5:118690659-118691201	GM12878	blood:	n/a	n/a
32	SPI1	chr5:118690572-118690883	GM12891	blood:	n/a	n/a
33	POLR2A	chr5:118689533-118692735	GM18951	blood:	n/a	n/a
34	EBF1	chr5:118690736-118692045	GM12878	blood:	n/a	n/a
35	POLR2A	chr5:118690744-118692293	H1-hESC	embryonic stem cell:	n/a	n/a
36	ZNF143	chr5:118690625-118691127	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr5:118690398-118692628	GM12892	blood:	n/a	n/a
38	POLR2A	chr5:118690592-118692032	GM12891	blood:	n/a	n/a
39	TFAP2A	chr5:118690770-118691264	Hela-S3	cervix:	n/a	chr5:118691034-118691042 chr5:118691031-118691045 chr5:118691034-118691042 chr5:118691034-118691042 chr5:118691031-118691046 chr5:118691031-118691045 chr5:118691031-118691045
40	MTA3	chr5:118688980-118694183	GM12878	blood:	n/a	n/a
41	TCF7L2	chr5:118690720-118691408	Hela-S3	cervix:	n/a	n/a
42	TFAP2C	chr5:118690665-118691276	Hela-S3	cervix:	n/a	chr5:118691031-118691046
43	BHLHE40	chr5:118690758-118692466	GM12878	blood:	n/a	chr5:118691457-118691473 chr5:118691449-118691465
44	SPI1	chr5:118690300-118690938	GM12891	blood:	n/a	n/a
45	RCOR1	chr5:118690415-118690837	GM12878	blood:	n/a	n/a
46	TBP	chr5:118690741-118691993	H1-hESC	embryonic stem cell:	n/a	n/a
47	SMARCB1	chr5:118690698-118692057	Hela-S3	cervix:	n/a	n/a
48	NFIC	chr5:118689422-118691329	GM12878	blood:	n/a	n/a
49	SMC3	chr5:118690658-118690804	GM12878	blood:	n/a	n/a
50	SPI1	chr5:118690112-118691013	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TNFAIP8	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10059175	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs10477585	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1112247	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11949608	0.86[CHB][hapmap]
rs13155880	0.87[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1396609	0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs17145265	0.89[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes]
rs250298	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs250299	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs250308	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32653	0.87[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32655	0.97[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32657	0.97[AFR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs32658	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3797339	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3797341	0.87[AFR][1000 genomes]
rs3797343	0.83[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs3920174	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs408095	0.88[ASW][hapmap];0.83[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs461108	0.80[GIH][hapmap]
rs4895372	0.81[JPT][hapmap]
rs67328001	0.82[AFR][1000 genomes]
rs6863311	0.85[AFR][1000 genomes]
rs6864305	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs6869512	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs6870253	0.87[YRI][hapmap]
rs6876224	0.95[LWK][hapmap];0.80[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6877025	0.86[LWK][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs6882237	0.85[AFR][1000 genomes]
rs6891084	0.85[AFR][1000 genomes]
rs6896277	0.86[AFR][1000 genomes]
rs6896553	0.92[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs6896559	0.86[AFR][1000 genomes]
rs7707470	0.85[AFR][1000 genomes]
rs996934	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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:91 , 50 per page) page: 1 2

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	chr5:118679000-118690800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr5:118680800-118691000	Weak transcription	HSMMtube	muscle
6	chr5:118682600-118693600	Weak transcription	Dnd41	blood
7	chr5:118684000-118690800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:118684000-118691000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:118684000-118691000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:118684000-118692800	Weak transcription	K562	blood
11	chr5:118684200-118691000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr5:118685000-118691000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:118685400-118690800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:118687200-118690800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr5:118687800-118691000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr5:118687800-118691000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr5:118688000-118691000	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr5:118688200-118690800	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr5:118688600-118691200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:118688800-118691000	Enhancers	Adipose Nuclei	Adipose
21	chr5:118688800-118691400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:118689000-118690800	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr5:118689000-118691000	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr5:118689000-118691000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:118689000-118691000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr5:118689000-118691000	Enhancers	Fetal Stomach	stomach
27	chr5:118689000-118691200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr5:118689000-118691200	Enhancers	Placenta	Placenta
29	chr5:118689000-118691200	Enhancers	NHDF-Ad	bronchial
30	chr5:118689000-118691400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr5:118689200-118690800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:118689200-118691000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr5:118689200-118691200	Enhancers	Fetal Heart	heart
34	chr5:118689400-118691000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:118689400-118691200	Enhancers	Fetal Thymus	thymus
36	chr5:118689400-118691400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:118689600-118690800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
38	chr5:118689600-118691000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:118689600-118691200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr5:118689600-118692000	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr5:118689800-118690800	Weak transcription	Esophagus	oesophagus
42	chr5:118689800-118691000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
43	chr5:118689800-118691000	Enhancers	Primary hematopoietic stem cells	blood
44	chr5:118689800-118691000	Enhancers	Colon Smooth Muscle	Colon
45	chr5:118689800-118691000	Weak transcription	Spleen	Spleen
46	chr5:118689800-118691200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr5:118689800-118691200	Enhancers	Fetal Lung	lung
48	chr5:118690000-118690800	Enhancers	Primary T cells fromperipheralblood	blood
49	chr5:118690000-118690800	Enhancers	Stomach Smooth Muscle	stomach
50	chr5:118690000-118691000	Weak transcription	H9 Cell Line	embryonic stem cell

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