Variant report

Variant	rs17102327
Chromosome Location	chr12:66672961-66672962
allele	C/T
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	chr12:66672930-66673280	K562	blood:	n/a	chr12:66673102-66673116
2	SMC3	chr12:66672930-66673280	GM12878	blood:	n/a	chr12:66673102-66673116
3	RAD21	chr12:66672889-66673290	A549	lung:	n/a	chr12:66673101-66673120
4	CTCF	chr12:66672873-66673269	K562	blood:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
5	CTCF	chr12:66672905-66673190	H1-hESC	embryonic stem cell:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
6	RAD21	chr12:66672837-66673334	MCF-7	breast:	n/a	chr12:66673101-66673120
7	CTCF	chr12:66672916-66673292	K562	blood:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
8	CTCF	chr12:66672878-66673366	MCF-7	breast:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
9	MAZ	chr12:66672932-66673249	K562	blood:	n/a	n/a
10	RAD21	chr12:66672443-66673495	SK-N-SH	brain:	n/a	chr12:66673101-66673120
11	CTCF	chr12:66672945-66673243	MCF-7	breast:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
12	RAD21	chr12:66672921-66673219	GM12878	blood:	n/a	chr12:66673101-66673120
13	RAD21	chr12:66672961-66673252	Hela-S3	cervix:	n/a	chr12:66673101-66673120
14	CTCF	chr12:66672851-66673373	HCT-116	colon:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
15	CTCF	chr12:66672886-66673258	H1-hESC	embryonic stem cell:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
16	USF2	chr12:66672900-66672999	HepG2	liver:	n/a	n/a
17	RAD21	chr12:66672844-66673306	SK-N-SH_RA	brain:	n/a	chr12:66673101-66673120
18	RAD21	chr12:66672924-66673291	H1-hESC	embryonic stem cell:	n/a	chr12:66673101-66673120
19	RAD21	chr12:66672817-66673398	MCF-7	breast:	n/a	chr12:66673101-66673120
20	ZNF143	chr12:66672938-66673238	K562	blood:	n/a	n/a
21	CTCF	chr12:66672922-66673245	A549	lung:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
22	CTCF	chr12:66672958-66673230	MCF-7	breast:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
23	CTCF	chr12:66672763-66673493	HCT-116	colon:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
24	RAD21	chr12:66672924-66673282	HepG2	liver:	n/a	chr12:66673101-66673120
25	RAD21	chr12:66672922-66673213	GM12878	blood:	n/a	chr12:66673101-66673120
26	SMC3	chr12:66672952-66673259	Hela-S3	cervix:	n/a	chr12:66673102-66673116
27	RAD21	chr12:66672894-66673219	SK-N-SH_RA	brain:	n/a	chr12:66673101-66673120
28	RAD21	chr12:66672938-66673277	GM12878	blood:	n/a	chr12:66673101-66673120
29	RAD21	chr12:66672871-66673491	HCT-116	colon:	n/a	chr12:66673101-66673120
30	RAD21	chr12:66672910-66673336	HepG2	liver:	n/a	chr12:66673101-66673120
31	RAD21	chr12:66672918-66673255	H1-hESC	embryonic stem cell:	n/a	chr12:66673101-66673120
32	RAD21	chr12:66672875-66673307	ECC-1	luminal epithelium:	n/a	chr12:66673101-66673120
33	RAD21	chr12:66672933-66673274	IMR90	lung:	n/a	chr12:66673101-66673120
34	CTCF	chr12:66672714-66673429	A549	lung:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
35	CTCF	chr12:66672951-66673244	Spleen_OC	spleen:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
36	CTCF	chr12:66672913-66673295	GM12878	blood:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
37	CTCF	chr12:66672919-66673234	K562	blood:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
38	SMC3	chr12:66672854-66673401	SK-N-SH	brain:	n/a	chr12:66673102-66673116
39	CTCF	chr12:66672800-66673451	SK-N-SH	brain:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
40	E2F4	chr12:66672960-66673153	MCF10A-Er-Src	breast:	n/a	n/a
41	CTCF	chr12:66672912-66673276	K562	blood:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
42	RAD21	chr12:66672855-66673384	ECC-1	luminal epithelium:	n/a	chr12:66673101-66673120
43	RAD21	chr12:66672917-66673279	A549	lung:	n/a	chr12:66673101-66673120
44	CTCF	chr12:66672853-66673260	MCF-7	breast:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
45	CTCF	chr12:66672902-66673305	IMR90	lung:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
46	RAD21	chr12:66672854-66673449	HCT-116	colon:	n/a	chr12:66673101-66673120
47	SMC3	chr12:66672917-66673263	HepG2	liver:	n/a	chr12:66673102-66673116
48	CTCF	chr12:66672864-66673239	HepG2	liver:	n/a	chr12:66673102-66673123 chr12:66673100-66673118
49	CTCF	chr12:66672940-66673090	GM12871	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:66672595..66673805-chr12:66802877..66803711,5	MCF-7	breast:
2	chr12:66561793..66564374-chr12:66672435..66674661,2	MCF-7	breast:

Variant related genes	Relation type
PDCL3P7	TF binding region
ENSG00000155957	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11833001	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11834499	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11835153	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11837166	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17102322	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17102326	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17102332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7132435	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7133184	0.84[AFR][1000 genomes]
rs7135616	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7137615	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7137685	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7296320	0.84[AFR][1000 genomes]
rs7308551	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7308914	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs74100138	1.00[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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv899216	chr12:66563835-66716844	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats 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 miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66664400-66673000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:66664600-66673000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr12:66669600-66673000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr12:66670200-66673000	Weak transcription	Primary T cells from cord blood	blood
5	chr12:66672400-66673000	Enhancers	HUVEC	blood vessel
6	chr12:66672600-66674800	Enhancers	Monocytes-CD14+_RO01746	blood
7	chr12:66672600-66675000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr12:66672800-66675000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:66672800-66675200	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr12:66672800-66675200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:66672800-66675200	Enhancers	Primary T helper cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links