Variant report

Variant	rs4276369
Chromosome Location	chr5:60625875-60625876
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	BCL3	chr5:60625611-60626095	GM12878	blood:	n/a	n/a
2	FOSL2	chr5:60625676-60626011	HepG2	liver:	n/a	chr5:60625806-60625817
3	REST	chr5:60625830-60631210	H1-neurons	neurons:	n/a	chr5:60629395-60629408 chr5:60626655-60626668
4	NR2F2	chr5:60625714-60625886	K562	blood:	n/a	n/a
5	FOS	chr5:60625702-60625989	MCF10A-Er-Src	breast:	n/a	chr5:60625807-60625818
6	MYC	chr5:60625746-60626233	MCF10A-Er-Src	breast:	n/a	n/a
7	FOSL2	chr5:60625558-60625968	HepG2	liver:	n/a	chr5:60625806-60625817
8	POLR2A	chr5:60625566-60625978	HUVEC	blood vessel:	n/a	n/a
9	FOS	chr5:60625382-60626284	HUVEC	blood vessel:	n/a	chr5:60625807-60625818
10	POLR2A	chr5:60625558-60630285	Hela-S3	cervix:	n/a	n/a
11	MAFK	chr5:60625724-60627683	Hela-S3	cervix:	n/a	chr5:60626128-60626143
12	MAZ	chr5:60625705-60625905	GM12878	blood:	n/a	n/a
13	POLR2A	chr5:60625341-60628382	HUVEC	blood vessel:	n/a	n/a
14	RCOR1	chr5:60625772-60625971	GM12878	blood:	n/a	n/a
15	GATA2	chr5:60625552-60626658	HUVEC	blood vessel:	n/a	n/a
16	ARID3A	chr5:60625693-60625919	HepG2	liver:	n/a	n/a
17	FOXM1	chr5:60625631-60626062	GM12878	blood:	n/a	n/a
18	MXI1	chr5:60625150-60628551	IMR90	lung:	n/a	n/a
19	TBL1XR1	chr5:60625682-60625966	GM12878	blood:	n/a	n/a
20	EP300	chr5:60625697-60626027	Hela-S3	cervix:	n/a	n/a
21	RCOR1	chr5:60623071-60628252	IMR90	lung:	n/a	n/a
22	CHD1	chr5:60623202-60631624	IMR90	lung:	n/a	chr5:60629730-60629740 chr5:60629024-60629034 chr5:60629683-60629693 chr5:60629116-60629123 chr5:60629352-60629362 chr5:60627826-60627836
23	POLR2A	chr5:60625830-60625899	MCF10A-Er-Src	breast:	n/a	n/a
24	BATF	chr5:60625621-60625966	GM12878	blood:	n/a	chr5:60625809-60625820
25	BCL3	chr5:60625662-60625919	GM12878	blood:	n/a	n/a
26	PAX5	chr5:60625639-60625983	GM12878	blood:	n/a	n/a
27	PBX3	chr5:60625739-60625929	GM12878	blood:	n/a	n/a
28	STAT3	chr5:60625732-60625966	MCF10A-Er-Src	breast:	n/a	n/a
29	KAP1	chr5:60624848-60626830	HEK293	kidney:	n/a	n/a
30	RAD21	chr5:60625559-60627319	Hela-S3	cervix:	n/a	n/a
31	BATF	chr5:60625609-60625976	GM12878	blood:	n/a	chr5:60625809-60625820
32	FOS	chr5:60625640-60626463	MCF10A-Er-Src	breast:	n/a	chr5:60625807-60625818
33	ZKSCAN1	chr5:60625470-60625982	Hela-S3	cervix:	n/a	n/a
34	PAX5	chr5:60625712-60625961	GM12878	blood:	n/a	n/a
35	KAP1	chr5:60625602-60626704	U2OS	brain:	n/a	n/a
36	EP300	chr5:60625685-60626011	GM12878	blood:	n/a	n/a
37	TBP	chr5:60625754-60625981	GM12878	blood:	n/a	n/a
38	POLR2A	chr5:60625447-60627903	HUVEC	blood vessel:	n/a	n/a
39	RFX5	chr5:60625804-60628207	Hela-S3	cervix:	n/a	n/a
40	JUN	chr5:60625746-60625991	HepG2	liver:	n/a	n/a
41	EBF1	chr5:60625677-60625965	GM12878	blood:	n/a	n/a
42	EP300	chr5:60625721-60625965	GM12878	blood:	n/a	n/a
43	MXI1	chr5:60625218-60631493	SK-N-SH	brain:	n/a	n/a
44	SMC3	chr5:60625505-60627719	Hela-S3	cervix:	n/a	chr5:60627693-60627703 chr5:60626856-60626870 chr5:60625619-60625626 chr5:60626837-60626847 chr5:60626859-60626869
45	JUND	chr5:60625689-60625953	HepG2	liver:	n/a	chr5:60625807-60625818
46	FOS	chr5:60625664-60625985	MCF10A-Er-Src	breast:	n/a	chr5:60625807-60625818
47	NFIC	chr5:60625604-60626077	GM12878	blood:	n/a	n/a
48	POLR2A	chr5:60623868-60631522	IMR90	lung:	n/a	n/a
49	STAT3	chr5:60625694-60626071	Hela-S3	cervix:	n/a	chr5:60626045-60626056
50	HCFC1	chr5:60625212-60628404	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:60454421..60471345-chr5:60622342..60633215,36	MCF-7	breast:
2	chr5:60454193..60465680-chr5:60622262..60629761,38	MCF-7	breast:
3	chr5:60469553..60471380-chr5:60625380..60627759,2	MCF-7	breast:
4	chr12:53845725..53846383-chr5:60625600..60626600,2	Hela-S3	cervix:
5	chr5:60546830..60548400-chr5:60625408..60627597,2	MCF-7	breast:
6	chr5:60353410..60356120-chr5:60624338..60627119,3	MCF-7	breast:
7	chr5:60623389..60626002-chr5:60627972..60629688,3	K562	blood:
8	chr5:60554941..60557365-chr5:60625053..60627690,3	MCF-7	breast:
9	chr5:60605123..60607843-chr5:60623875..60626572,3	MCF-7	breast:

Variant related genes	Relation type
ZSWIM6	TF binding region
ENSG00000197111	Chromatin interaction
ENSG00000130449	Chromatin interaction
ENSG00000251279	Chromatin interaction
ENSG00000188725	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10041978	0.82[ASN][1000 genomes]
rs10939900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939901	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10939902	0.94[ASN][1000 genomes]
rs10939903	0.82[ASN][1000 genomes]
rs11743711	0.84[ASN][1000 genomes]
rs11750589	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11950318	0.80[ASN][1000 genomes]
rs11952146	0.94[JPT][hapmap]
rs12187112	0.89[ASN][1000 genomes]
rs12188627	0.88[ASN][1000 genomes]
rs12189001	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12518479	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12520628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12522647	0.82[ASN][1000 genomes]
rs13158675	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13162358	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13169711	0.95[ASN][1000 genomes]
rs13170135	0.93[ASN][1000 genomes]
rs13171757	0.84[ASN][1000 genomes]
rs13172084	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs13178686	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13181015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13186194	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs13188327	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1445979	0.82[ASN][1000 genomes]
rs1477355	0.82[ASN][1000 genomes]
rs28610339	0.94[ASN][1000 genomes]
rs34739794	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35262187	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4392578	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4484384	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4604142	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs5027472	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56035042	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60529601	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60886975	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62368660	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6449527	0.81[CEU][hapmap]
rs6449528	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6449529	0.95[ASN][1000 genomes]
rs6449530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6449531	0.94[ASN][1000 genomes]
rs6449532	0.94[ASN][1000 genomes]
rs6449533	0.94[ASN][1000 genomes]
rs6449535	0.82[ASN][1000 genomes]
rs6860608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6873712	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6877610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6878927	0.94[JPT][hapmap]
rs6881765	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6885005	0.94[ASN][1000 genomes]
rs6890351	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6894675	0.94[ASN][1000 genomes]
rs7700289	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7701440	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7709645	0.94[ASN][1000 genomes]
rs7714712	0.94[ASN][1000 genomes]
rs7722810	0.83[ASN][1000 genomes]
rs7724551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7727824	0.94[ASN][1000 genomes]
rs7734879	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028884	chr5:60414723-60732779	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv823089	chr5:60589501-60669903	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv19714	chr5:60625377-60629756	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv3471610	chr5:60625845-60630243	Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	esv3471611	chr5:60625845-60630243	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60617000-60626200	Weak transcription	Esophagus	oesophagus
2	chr5:60619400-60626200	Weak transcription	Small Intestine	intestine
3	chr5:60623200-60626000	Enhancers	HMEC	breast
4	chr5:60623400-60626000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:60623600-60626000	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr5:60623600-60626000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr5:60623600-60626000	Enhancers	NHEK	skin
8	chr5:60623600-60626200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:60623800-60626200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:60623800-60626400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr5:60624000-60626000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:60624200-60626000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:60624200-60626000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:60624400-60626000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
15	chr5:60624400-60626000	Enhancers	Fetal Heart	heart
16	chr5:60624400-60626000	Enhancers	Placenta	Placenta
17	chr5:60624400-60626200	Bivalent Enhancer	GM12878-XiMat	blood
18	chr5:60624400-60626600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr5:60624600-60626000	Enhancers	Fetal Muscle Leg	muscle
20	chr5:60624600-60626000	Enhancers	Pancreas	Pancrea
21	chr5:60624600-60626000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr5:60624600-60626000	Enhancers	Stomach Mucosa	stomach
23	chr5:60624600-60626000	Flanking Active TSS	NHLF	lung
24	chr5:60624800-60626000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr5:60624800-60626200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
26	chr5:60624800-60626200	Enhancers	Placenta Amnion	Placenta Amnion
27	chr5:60625000-60626000	Enhancers	Primary B cells from peripheral blood	blood
28	chr5:60625000-60626000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:60625000-60626000	Weak transcription	Right Atrium	heart
30	chr5:60625000-60626800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
31	chr5:60625200-60626000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
32	chr5:60625200-60626000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
33	chr5:60625200-60626000	Enhancers	Fetal Muscle Trunk	muscle
34	chr5:60625200-60626000	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr5:60625200-60626000	Flanking Active TSS	Hela-S3	cervix
36	chr5:60625200-60626200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr5:60625200-60626200	Flanking Active TSS	A549	lung
38	chr5:60625200-60626600	Flanking Active TSS	HUVEC	blood vessel
39	chr5:60625200-60630800	Active TSS	Colonic Mucosa	Colon
40	chr5:60625400-60626000	Enhancers	Primary hematopoietic stem cells	blood
41	chr5:60625400-60626000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:60625400-60626000	Weak transcription	Ovary	ovary
43	chr5:60625400-60626000	Weak transcription	Right Ventricle	heart
44	chr5:60625400-60626200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr5:60625400-60626200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
46	chr5:60625400-60626200	Weak transcription	Left Ventricle	heart
47	chr5:60625400-60626200	Weak transcription	Lung	lung
48	chr5:60625400-60626200	Weak transcription	Spleen	Spleen
49	chr5:60625400-60626400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr5:60625400-60626400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum

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