Variant report

Variant	rs3753555
Chromosome Location	chr1:175162805-175162806
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	CTBP2	chr1:175161323-175163077	H1-hESC	embryonic stem cell:	n/a	n/a
2	SMARCC1	chr1:175161173-175163079	Hela-S3	cervix:	n/a	n/a
3	IRF1	chr1:175160797-175162815	K562	blood:	n/a	chr1:175161058-175161071 chr1:175161058-175161072 chr1:175161057-175161071 chr1:175162259-175162273 chr1:175161053-175161067 chr1:175161057-175161077 chr1:175161059-175161073 chr1:175161338-175161351 chr1:175161051-175161071 chr1:175161058-175161071 chr1:175161057-175161070 chr1:175161053-175161070 chr1:175161055-175161069 chr1:175161059-175161069
4	FOS	chr1:175162713-175163008	MCF10A-Er-Src	breast:	n/a	n/a
5	ZNF263	chr1:175160625-175163127	HEK293-T-REx	kidney:	n/a	chr1:175160916-175160925
6	POLR2A	chr1:175160872-175162810	MCF10A-Er-Src	breast:	n/a	n/a
7	STAT1	chr1:175161083-175163061	Hela-S3	cervix:	n/a	chr1:175162373-175162382 chr1:175162441-175162452 chr1:175162443-175162452 chr1:175162442-175162451 chr1:175162372-175162381 chr1:175162409-175162420 chr1:175162259-175162271
8	POLR2A	chr1:175160620-175163581	MCF10A-Er-Src	breast:	n/a	n/a
9	E2F6	chr1:175161965-175162951	H1-hESC	embryonic stem cell:	n/a	chr1:175162263-175162272 chr1:175162260-175162272 chr1:175162225-175162236 chr1:175162238-175162249
10	MYC	chr1:175161995-175162921	MCF10A-Er-Src	breast:	n/a	n/a
11	MYC	chr1:175161324-175163163	K562	blood:	n/a	n/a
12	SMARCB1	chr1:175161292-175163080	Hela-S3	cervix:	n/a	n/a
13	MAX	chr1:175162450-175163032	H1-hESC	embryonic stem cell:	n/a	n/a
14	STAT3	chr1:175162108-175162913	MCF10A-Er-Src	breast:	n/a	chr1:175162373-175162382 chr1:175162441-175162452 chr1:175162443-175162452 chr1:175162442-175162451 chr1:175162372-175162381 chr1:175162259-175162271 chr1:175162409-175162420
15	SIN3A	chr1:175160857-175162830	H1-hESC	embryonic stem cell:	n/a	chr1:175162635-175162643 chr1:175162633-175162642
16	E2F6	chr1:175161490-175163008	K562	blood:	n/a	chr1:175162263-175162272 chr1:175162260-175162272 chr1:175162225-175162236 chr1:175162238-175162249
17	STAT3	chr1:175162061-175162933	MCF10A-Er-Src	breast:	n/a	chr1:175162373-175162382 chr1:175162441-175162452 chr1:175162443-175162452 chr1:175162442-175162451 chr1:175162372-175162381 chr1:175162259-175162271 chr1:175162409-175162420
18	ZEB1	chr1:175162708-175163129	GM12878	blood:	n/a	n/a
19	MYC	chr1:175162381-175163725	MCF10A-Er-Src	breast:	n/a	chr1:175163159-175163172 chr1:175163159-175163172 chr1:175163160-175163170 chr1:175163160-175163171 chr1:175163159-175163172 chr1:175163160-175163171 chr1:175163161-175163170 chr1:175163160-175163170 chr1:175163161-175163170 chr1:175163160-175163171 chr1:175163159-175163172 chr1:175163161-175163171 chr1:175163161-175163170 chr1:175163160-175163169 chr1:175163161-175163171 chr1:175163160-175163171
20	FOS	chr1:175162725-175163000	MCF10A-Er-Src	breast:	n/a	n/a
21	BHLHE40	chr1:175161449-175163027	K562	blood:	n/a	n/a
22	STAT3	chr1:175162076-175163008	MCF10A-Er-Src	breast:	n/a	chr1:175162373-175162382 chr1:175162441-175162452 chr1:175162443-175162452 chr1:175162442-175162451 chr1:175162372-175162381 chr1:175162259-175162271 chr1:175162409-175162420
23	STAT3	chr1:175162228-175162965	MCF10A-Er-Src	breast:	n/a	chr1:175162373-175162382 chr1:175162441-175162452 chr1:175162443-175162452 chr1:175162442-175162451 chr1:175162372-175162381 chr1:175162259-175162271 chr1:175162409-175162420
24	FOS	chr1:175162717-175163007	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:175152638..175154572-chr1:175162288..175163836,2	K562	blood:
2	chr1:175162286..175164417-chr1:175190945..175192662,2	MCF-7	breast:

Variant related genes	Relation type
KIAA0040	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1057239	0.94[ASW][hapmap]
rs1057246	0.94[ASW][hapmap]
rs10798341	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10798342	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10912903	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11583687	0.94[ASW][hapmap]
rs12084108	0.84[ASN][1000 genomes]
rs12143530	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1894709	0.94[ASW][hapmap]
rs2205603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2269650	0.81[GIH][hapmap]
rs2272784	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2685	0.94[ASW][hapmap]
rs34370567	0.94[ASW][hapmap]
rs3753554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3753557	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3766681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766683	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766685	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766687	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766688	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766692	0.84[ASN][1000 genomes]
rs3766694	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6674635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6677931	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6677935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs760486	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949473	chr1:175151666-175391741	Enhancers ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	esv15667	chr1:175161934-175163375	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3753555	KIFAP3	cis	cerebellum	SCAN
rs3753555	GORAB	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175160600-175163000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:175160600-175163200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr1:175160800-175163000	Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr1:175162200-175163000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr1:175162200-175163000	Enhancers	Sigmoid Colon	Sigmoid Colon
6	chr1:175162200-175163000	Enhancers	HSMMtube	muscle
7	chr1:175162200-175166400	Weak transcription	Spleen	Spleen
8	chr1:175162400-175163000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:175162400-175163000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:175162400-175163000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr1:175162400-175163000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:175162400-175163000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr1:175162400-175163000	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr1:175162400-175163000	Weak transcription	Small Intestine	intestine
15	chr1:175162400-175163000	Flanking Active TSS	Hela-S3	cervix
16	chr1:175162400-175163200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr1:175162400-175168000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:175162600-175163000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:175162600-175163000	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:175162600-175163000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:175162600-175163000	Enhancers	Muscle Satellite Cultured Cells	--
22	chr1:175162600-175163000	Enhancers	Colonic Mucosa	Colon
23	chr1:175162600-175163000	Enhancers	Duodenum Mucosa	Duodenum
24	chr1:175162600-175163000	Enhancers	Esophagus	oesophagus
25	chr1:175162600-175163000	Enhancers	Fetal Stomach	stomach
26	chr1:175162600-175163000	Enhancers	Lung	lung
27	chr1:175162600-175163000	Enhancers	Right Ventricle	heart
28	chr1:175162600-175163000	Enhancers	HSMM	muscle
29	chr1:175162600-175163000	Enhancers	NH-A	brain
30	chr1:175162600-175163200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:175162600-175163200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:175162600-175163200	Enhancers	Primary hematopoietic stem cells	blood
33	chr1:175162600-175163200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:175162600-175163200	Enhancers	Fetal Intestine Small	intestine
35	chr1:175162600-175163200	Enhancers	Fetal Muscle Leg	muscle
36	chr1:175162600-175163200	Enhancers	Placenta	Placenta
37	chr1:175162600-175163200	Enhancers	Fetal Thymus	thymus
38	chr1:175162600-175163200	Enhancers	Left Ventricle	heart
39	chr1:175162600-175163200	Enhancers	Pancreas	Pancrea
40	chr1:175162600-175163200	Enhancers	Stomach Mucosa	stomach
41	chr1:175162600-175163800	Enhancers	Primary neutrophils fromperipheralblood	blood
42	chr1:175162600-175163800	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr1:175162600-175164000	Enhancers	NHEK	skin
44	chr1:175162600-175164200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:175162600-175164600	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr1:175162600-175164600	Enhancers	GM12878-XiMat	blood
47	chr1:175162600-175166400	Weak transcription	Primary T cells from cord blood	blood
48	chr1:175162600-175166400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:175162600-175166600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:175162600-175167800	Enhancers	Primary B cells from peripheral blood	blood

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