Variant report

Variant	rs55670246
Chromosome Location	chr3:119318927-119318928
allele	A/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	SMC3	chr3:119318923-119320065	SK-N-SH	brain:	n/a	chr3:119319716-119319723
2	RCOR1	chr3:119318598-119320246	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:119315795-119320559	GM12878	blood:	n/a	n/a
4	EBF1	chr3:119316230-119320348	GM12878	blood:	n/a	chr3:119317324-119317335
5	MXI1	chr3:119318429-119320463	GM12878	blood:	n/a	n/a
6	POLR2A	chr3:119316322-119320295	GM12891	blood:	n/a	n/a
7	STAT5A	chr3:119317078-119319327	GM12878	blood:	n/a	chr3:119318677-119318689 chr3:119319078-119319086
8	ATF2	chr3:119316171-119318970	GM12878	blood:	n/a	n/a
9	EP300	chr3:119318185-119319348	GM12878	blood:	n/a	n/a
10	NFIC	chr3:119315804-119319171	GM12878	blood:	n/a	n/a
11	POLR2A	chr3:119317245-119320053	GM12892	blood:	n/a	n/a
12	NFATC1	chr3:119318315-119320367	GM12878	blood:	n/a	chr3:119320219-119320233
13	POLR2A	chr3:119316342-119320274	GM18951	blood:	n/a	n/a
14	PML	chr3:119314495-119320501	GM12878	blood:	n/a	n/a
15	RFX5	chr3:119318268-119319080	GM12878	blood:	n/a	n/a
16	CEBPB	chr3:119316601-119318949	GM12878	blood:	n/a	chr3:119317085-119317098
17	POLR2A	chr3:119317212-119319940	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:119318921-119320405	GM19193	blood:	n/a	n/a
19	POLR2A	chr3:119317138-119320307	GM12892	blood:	n/a	n/a
20	TBL1XR1	chr3:119318448-119320284	GM12878	blood:	n/a	n/a
21	CHD2	chr3:119316648-119319935	GM12878	blood:	n/a	n/a
22	WRNIP1	chr3:119317226-119320130	GM12878	blood:	n/a	n/a
23	NFATC1	chr3:119318316-119320499	GM12878	blood:	n/a	chr3:119320219-119320233
24	CHD1	chr3:119316263-119320189	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:119317333-119320090	GM12878	blood:	n/a	n/a
26	RELA	chr3:119316313-119319077	GM19099	blood:	n/a	n/a
27	SMC3	chr3:119318309-119318927	GM12878	blood:	n/a	n/a
28	ATF2	chr3:119318262-119320560	GM12878	blood:	n/a	n/a
29	MTA3	chr3:119317076-119319230	GM12878	blood:	n/a	n/a
30	POLR2A	chr3:119314772-119320568	GM12878	blood:	n/a	n/a
31	POLR2A	chr3:119315907-119320520	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:119316217-119320450	GM12878	blood:	n/a	n/a
33	MTA3	chr3:119315715-119320461	GM12878	blood:	n/a	n/a
34	FOXM1	chr3:119316121-119318989	GM12878	blood:	n/a	n/a
35	POLR2A	chr3:119317156-119320206	GM12892	blood:	n/a	n/a
36	POLR2A	chr3:119317181-119320325	GM12891	blood:	n/a	n/a
37	POLR2A	chr3:119317126-119320393	GM12892	blood:	n/a	n/a
38	ZNF143	chr3:119318865-119318974	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:119317178-119319396	GM12891	blood:	n/a	n/a
40	POLR2A	chr3:119317209-119320309	GM19099	blood:	n/a	n/a
41	POLR2A	chr3:119318900-119319292	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119297675..119300178-chr3:119317651..119319596,4	MCF-7	breast:

Variant related genes	Relation type
PLA1A	TF binding region
ENSG00000272967	Chromatin interaction
ENSG00000144843	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10433338	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13443	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1525838	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1534154	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1723969	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1797831	0.96[ASN][1000 genomes]
rs1797832	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2049501	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs20569	0.80[EUR][1000 genomes]
rs2171025	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2248483	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2251566	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2272267	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272268	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272269	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2272270	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2629399	0.96[ASN][1000 genomes]
rs2629400	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2629408	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2670293	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2670298	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688637	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688638	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688639	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688646	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688647	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688648	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692612	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692613	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2692614	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692615	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2692621	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2692623	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs474926	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs485257	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs487124	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs528765	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs530389	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530783	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs536624	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs538136	0.97[ASN][1000 genomes]
rs551885	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs555525	1.00[ASN][1000 genomes]
rs55801535	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56197198	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58020513	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs593968	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666134	0.95[ASN][1000 genomes]
rs6807201	0.96[ASN][1000 genomes]
rs6807613	0.94[ASN][1000 genomes]
rs72954966	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv1831824	chr3:119263607-119402474	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv3963	chr3:119301064-119345904	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv591363	chr3:119316828-119345950	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119310600-119319800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:119315000-119320200	Enhancers	Left Ventricle	heart
3	chr3:119315400-119319200	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:119315600-119319000	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr3:119315600-119319600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:119316000-119319200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:119316200-119319400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:119316200-119319400	Weak transcription	Placenta	Placenta
9	chr3:119316200-119319600	Weak transcription	Spleen	Spleen
10	chr3:119316200-119340600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:119316400-119320600	Flanking Active TSS	GM12878-XiMat	blood
12	chr3:119316600-119320200	Enhancers	Right Ventricle	heart
13	chr3:119317000-119319000	Enhancers	Fetal Intestine Large	intestine
14	chr3:119317000-119319800	Weak transcription	Fetal Lung	lung
15	chr3:119317000-119319800	Weak transcription	HepG2	liver
16	chr3:119317000-119323800	Weak transcription	HSMMtube	muscle
17	chr3:119317200-119320200	Enhancers	Right Atrium	heart
18	chr3:119317200-119321200	Weak transcription	HUVEC	blood vessel
19	chr3:119317400-119319600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:119317400-119320200	Enhancers	Lung	lung
21	chr3:119317600-119320000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:119317600-119327800	Weak transcription	Fetal Intestine Small	intestine
23	chr3:119317800-119319400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:119318000-119319600	Weak transcription	Psoas Muscle	Psoas
25	chr3:119318000-119320600	Enhancers	Fetal Heart	heart
26	chr3:119318400-119321600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:119318400-119321600	Weak transcription	Gastric	stomach
28	chr3:119318400-119321800	Weak transcription	Pancreas	Pancrea
29	chr3:119318600-119344200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:119318800-119319000	Enhancers	Adipose Nuclei	Adipose
31	chr3:119318800-119327800	Weak transcription	Liver	Liver

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