Variant report

Variant	rs12296922
Chromosome Location	chr12:58289885-58289886
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:4)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:58288646-58291559	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr12:58289665-58289994	U87	brain:	n/a	n/a
3	POLR2A	chr12:58289450-58291018	U87	brain:	n/a	n/a
4	SMC3	chr12:58289586-58291477	SK-N-SH	brain:	n/a	chr12:58291369-58291379
5	RAD21	chr12:58289507-58290267	IMR90	lung:	n/a	n/a
6	EGR1	chr12:58289719-58290026	K562	blood:	n/a	n/a
7	RAD21	chr12:58289720-58291548	SK-N-SH	brain:	n/a	chr12:58290718-58290728 chr12:58291323-58291335 chr12:58291514-58291528
8	POLR2A	chr12:58289793-58290780	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr12:58289665-58290049	U87	brain:	n/a	n/a
10	MAZ	chr12:58289185-58291043	IMR90	lung:	n/a	chr12:58290564-58290577
11	ZBTB7A	chr12:58289872-58291151	ECC-1	luminal epithelium:	n/a	n/a
12	WRNIP1	chr12:58289758-58290018	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:58289841-58290703	U87	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58238802..58241111-chr12:58289482..58291156,2	K562	blood:
2	chr12:58238695..58240382-chr12:58287823..58289916,2	K562	blood:
3	chr12:58236711..58242486-chr12:58286970..58293951,15	MCF-7	breast:
4	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:

(count:4 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CTDSP2-1	chr12:58287523-58290265	ENSG00000245651
2	lnc-XRCC6BP1-1	chr12:58289435-58290670	XLOC_009779
3	lnc-CTDSP2-1	chr12:58287523-58290267	XLOC_010101
4	lnc-CTDSP2-1	chr12:58287523-58290265	ENSG00000245651

No data

Variant related genes	Relation type
ENSG00000245651	TF binding region
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11172376	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172377	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11834260	0.95[ASN][1000 genomes]
rs12309291	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12322495	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322586	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17119981	0.95[ASN][1000 genomes]
rs17119991	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34241380	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34372362	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35441007	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35985500	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61935768	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58285600-58290000	Enhancers	Brain Angular Gyrus	brain
2	chr12:58285600-58290000	Enhancers	Left Ventricle	heart
3	chr12:58285600-58290200	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr12:58285800-58290000	Enhancers	Placenta	Placenta
5	chr12:58285800-58290000	Enhancers	Right Atrium	heart
6	chr12:58285800-58290000	Enhancers	Right Ventricle	heart
7	chr12:58285800-58290200	Enhancers	Lung	lung
8	chr12:58286000-58290600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr12:58286200-58290000	Enhancers	Fetal Thymus	thymus
10	chr12:58286600-58290200	Enhancers	Placenta Amnion	Placenta Amnion
11	chr12:58286800-58291400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr12:58287000-58290000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:58287200-58290000	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr12:58287200-58290000	Enhancers	Pancreas	Pancrea
15	chr12:58287200-58290000	Enhancers	Psoas Muscle	Psoas
16	chr12:58287200-58290000	Enhancers	NH-A	brain
17	chr12:58287200-58290200	Flanking Active TSS	Rectal Smooth Muscle	rectum
18	chr12:58287400-58290000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:58287400-58290000	Enhancers	Primary hematopoietic stem cells	blood
20	chr12:58287600-58290000	Enhancers	Primary B cells from peripheral blood	blood
21	chr12:58287600-58290000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr12:58287800-58290000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr12:58287800-58290000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:58287800-58290400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:58287800-58290400	Flanking Active TSS	NHDF-Ad	bronchial
26	chr12:58288000-58290000	Enhancers	Colonic Mucosa	Colon
27	chr12:58288000-58290200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:58288200-58290000	Enhancers	Primary T cells fromperipheralblood	blood
29	chr12:58288200-58290000	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr12:58288200-58290000	Enhancers	Ovary	ovary
31	chr12:58288200-58290000	Enhancers	HSMMtube	muscle
32	chr12:58288200-58290200	Enhancers	Primary B cells from cord blood	blood
33	chr12:58288200-58290200	Enhancers	Small Intestine	intestine
34	chr12:58288200-58290200	Enhancers	GM12878-XiMat	blood
35	chr12:58288200-58293200	Enhancers	Spleen	Spleen
36	chr12:58288400-58290000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:58288400-58290000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr12:58288400-58290000	Enhancers	Fetal Heart	heart
39	chr12:58288400-58290000	Enhancers	Fetal Intestine Small	intestine
40	chr12:58288400-58290000	Enhancers	Fetal Muscle Leg	muscle
41	chr12:58288400-58290000	Bivalent Enhancer	HepG2	liver
42	chr12:58288400-58290200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:58288400-58290200	Enhancers	Fetal Kidney	kidney
44	chr12:58288400-58290600	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr12:58288400-58291000	Weak transcription	K562	blood
46	chr12:58288400-58292000	Weak transcription	Hela-S3	cervix
47	chr12:58288600-58290000	Enhancers	Fetal Intestine Large	intestine
48	chr12:58288600-58290000	Enhancers	Fetal Muscle Trunk	muscle
49	chr12:58288800-58290000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr12:58288800-58290200	Flanking Active TSS	Fetal Brain Male	brain

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