Variant report

Variant	rs12520436
Chromosome Location	chr5:146719042-146719043
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:103)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:103 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr5:146719000-146719150	HCFaa	heart:	n/a	n/a
2	CTCF	chr5:146718911-146719177	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr5:146719011-146719139	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr5:146719000-146719150	GM12867	blood:	n/a	n/a
5	CTCF	chr5:146718960-146719110	GM12873	blood:	n/a	n/a
6	CTCF	chr5:146718980-146719130	GM06990	blood:	n/a	n/a
7	CTCF	chr5:146718980-146719130	GM12866	blood:	n/a	n/a
8	CTCF	chr5:146719000-146719150	GM12873	blood:	n/a	n/a
9	CTCF	chr5:146719020-146719170	GM12874	blood:	n/a	n/a
10	CTCF	chr5:146719020-146719170	GM06990	blood:	n/a	n/a
11	CTCF	chr5:146719000-146719150	AG09319	gingival:	n/a	n/a
12	CTCF	chr5:146718956-146719200	GM12892	blood:	n/a	n/a
13	CTCF	chr5:146718962-146719147	HepG2	liver:	n/a	n/a
14	CTCF	chr5:146718980-146719130	GM12875	blood:	n/a	n/a
15	RAD21	chr5:146718803-146719252	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr5:146718937-146719216	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr5:146718960-146719110	GM12872	blood:	n/a	n/a
18	CTCF	chr5:146718994-146719158	HepG2	liver:	n/a	n/a
19	CTCF	chr5:146718920-146719070	HRPEpiC	eye:	n/a	n/a
20	CTCF	chr5:146718960-146719110	HMF	breast:	n/a	n/a
21	CTCF	chr5:146718914-146719283	HCT-116	colon:	n/a	n/a
22	CTCF	chr5:146719020-146719170	GM12873	blood:	n/a	n/a
23	CTCF	chr5:146718900-146719050	HVMF	connective:	n/a	n/a
24	CTCF	chr5:146719020-146719170	HPF	lung:	n/a	n/a
25	CTCF	chr5:146718982-146719165	HUVEC	blood vessel:	n/a	n/a
26	CTCF	chr5:146718980-146719130	NB4	blood:	n/a	n/a
27	CTCF	chr5:146719006-146719131	GM19239	blood:	n/a	n/a
28	CTCF	chr5:146718920-146719070	HBMEC	blood vessel:	n/a	n/a
29	CTCF	chr5:146718940-146719090	GM12871	blood:	n/a	n/a
30	CTCF	chr5:146719000-146719150	HFF	foreskin:	n/a	n/a
31	CTCF	chr5:146718980-146719130	GM12870	blood:	n/a	n/a
32	CTCF	chr5:146719020-146719170	BJ	skin:	n/a	n/a
33	RAD21	chr5:146718922-146719264	A549	lung:	n/a	n/a
34	CTCF	chr5:146719020-146719170	MCF-7	breast:	n/a	n/a
35	RAD21	chr5:146718819-146719306	HCT-116	colon:	n/a	n/a
36	CTCF	chr5:146718977-146719146	MCF-7	breast:	n/a	n/a
37	CTCF	chr5:146718980-146719130	RPTEC	kidney:	n/a	n/a
38	CTCF	chr5:146718970-146719144	GM12891	blood:	n/a	n/a
39	CTCF	chr5:146718960-146719110	HUVEC	blood vessel:	n/a	n/a
40	CTCF	chr5:146718940-146719090	GM12865	blood:	n/a	n/a
41	CTCF	chr5:146719007-146719083	K562	blood:	n/a	n/a
42	CTCF	chr5:146719020-146719170	HEK293	kidney:	n/a	n/a
43	CTCF	chr5:146718980-146719130	GM12869	blood:	n/a	n/a
44	RAD21	chr5:146718944-146719265	HCT-116	colon:	n/a	n/a
45	CTCF	chr5:146719040-146719190	HEK293	kidney:	n/a	n/a
46	CTCF	chr5:146718972-146719151	Hela-S3	cervix:	n/a	n/a
47	CTCF	chr5:146718956-146719204	Gliobla	brain:	n/a	n/a
48	CTCF	chr5:146718975-146719167	GM19240	blood:	n/a	n/a
49	CTCF	chr5:146718979-146719168	GM12878	blood:	n/a	n/a
50	CTCF	chr5:146719040-146719190	GM12874	blood:	n/a	n/a

No data

Variant related genes	Relation type
STK32A	TF binding region

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10041697	0.81[JPT][hapmap]
rs10042298	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10070932	0.86[JPT][hapmap]
rs10079191	0.80[JPT][hapmap]
rs10477336	0.86[JPT][hapmap]
rs10515580	0.86[JPT][hapmap]
rs10515581	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10515582	0.86[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10515583	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11167988	0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11167989	0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs11748615	0.86[JPT][hapmap]
rs11954789	0.87[JPT][hapmap]
rs12513884	0.84[AMR][1000 genomes]
rs12514269	0.81[JPT][hapmap]
rs12514302	0.81[CHB][hapmap]
rs12518250	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12519887	0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12520080	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12520257	0.94[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12522616	0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12651731	0.86[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes]
rs12659468	0.87[JPT][hapmap]
rs13170279	0.81[JPT][hapmap]
rs1424293	0.85[JPT][hapmap]
rs1432838	0.85[JPT][hapmap]
rs1544816	0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17106458	0.86[JPT][hapmap]
rs17106470	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17106482	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17106492	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17106560	0.81[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17106572	0.85[JPT][hapmap];0.89[AMR][1000 genomes]
rs17106575	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs17106590	0.84[AMR][1000 genomes]
rs17106592	0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs17106597	0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes]
rs17106606	0.84[AMR][1000 genomes]
rs1895566	1.00[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2400295	0.87[JPT][hapmap]
rs2895681	0.84[AMR][1000 genomes]
rs3749721	0.84[AMR][1000 genomes]
rs3805533	0.84[AMR][1000 genomes]
rs3805534	0.86[CHB][hapmap]
rs3805535	0.86[CHB][hapmap]
rs4642416	0.84[AMR][1000 genomes]
rs4705164	0.81[JPT][hapmap]
rs4705165	0.86[JPT][hapmap]
rs4705166	0.86[JPT][hapmap]
rs6872292	0.87[JPT][hapmap]
rs6884181	0.86[JPT][hapmap]
rs7707452	0.86[JPT][hapmap]
rs7714240	0.85[JPT][hapmap]
rs918797	0.80[JPT][hapmap]
rs918798	0.86[JPT][hapmap]
rs972302	0.85[JPT][hapmap];0.84[AMR][1000 genomes]
rs9885145	0.81[JPT][hapmap]

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	nsv1015804	chr5:146066000-146788233	Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv537915	chr5:146066000-146788233	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv519847	chr5:146166378-146812647	Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv599938	chr5:146169511-146806365	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv869238	chr5:146179403-146787986	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv2763507	chr5:146718961-146727485	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:146707600-146725600	Weak transcription	Pancreas	Pancrea
2	chr5:146713800-146720800	Weak transcription	Fetal Kidney	kidney
3	chr5:146717800-146721800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:146718600-146719200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:146718600-146719200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:146718800-146719200	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:146719000-146719800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links