Variant report

Variant	rs12321305
Chromosome Location	chr12:42984845-42984846
allele	C/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	NR2F2	chr12:42984229-42984882	MCF-7	breast:	n/a	n/a
2	MAFK	chr12:42984754-42984931	HepG2	liver:	n/a	chr12:42984863-42984878 chr12:42984868-42984879 chr12:42984868-42984879
3	EP300	chr12:42982235-42984855	ECC-1	luminal epithelium:	n/a	chr12:42982351-42982361 chr12:42983501-42983510 chr12:42983498-42983507 chr12:42984759-42984773
4	MAZ	chr12:42981376-42985082	IMR90	lung:	n/a	chr12:42983670-42983679 chr12:42984534-42984544
5	MAX	chr12:42982660-42984847	ECC-1	luminal epithelium:	n/a	chr12:42983670-42983679 chr12:42984534-42984544
6	TCF12	chr12:42983986-42984953	ECC-1	luminal epithelium:	n/a	n/a
7	SMC3	chr12:42982437-42984934	SK-N-SH	brain:	n/a	chr12:42982812-42982819 chr12:42984593-42984607 chr12:42982868-42982882
8	RAD21	chr12:42981077-42985218	SK-N-SH	brain:	n/a	chr12:42983223-42983235 chr12:42982867-42982886 chr12:42984597-42984607 chr12:42984597-42984609
9	MAFK	chr12:42984764-42984953	HepG2	liver:	n/a	chr12:42984863-42984878 chr12:42984868-42984879 chr12:42984868-42984879
10	MAX	chr12:42982586-42984897	ECC-1	luminal epithelium:	n/a	chr12:42983670-42983679 chr12:42984534-42984544
11	MXI1	chr12:42980685-42985161	SK-N-SH	brain:	n/a	chr12:42984253-42984268
12	CTCF	chr12:42984720-42984870	HMF	breast:	n/a	n/a
13	KAP1	chr12:42983881-42984910	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
PRICKLE1	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11181556	1.00[ASN][1000 genomes]
rs11181560	1.00[ASN][1000 genomes]
rs12228734	1.00[ASN][1000 genomes]
rs12309366	1.00[ASN][1000 genomes]
rs12320873	1.00[ASN][1000 genomes]
rs12321729	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2103410	1.00[ASN][1000 genomes]
rs55930021	0.87[ASN][1000 genomes]
rs56898852	1.00[ASN][1000 genomes]
rs7308904	0.87[ASN][1000 genomes]
rs7955255	0.94[ASN][1000 genomes]
rs7965297	1.00[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	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
2	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv832388	chr12:42878328-43087069	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv989438	chr12:42981066-42988699	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	esv3361465	chr12:42982310-42984858	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42980000-42985000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr12:42981200-42985000	Active TSS	Right Atrium	heart
3	chr12:42981600-42985000	Active TSS	Fetal Kidney	kidney
4	chr12:42982000-42985000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr12:42984000-42985000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr12:42984000-42985000	Flanking Active TSS	HUVEC	blood vessel
7	chr12:42984200-42985000	Flanking Active TSS	Brain Anterior Caudate	brain
8	chr12:42984200-42985000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
9	chr12:42984200-42985000	Flanking Bivalent TSS/Enh	Osteobl	bone
10	chr12:42984400-42985000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
11	chr12:42984400-42985000	Bivalent Enhancer	Fetal Brain Male	brain
12	chr12:42984400-42985200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
13	chr12:42984400-42987200	Weak transcription	Gastric	stomach
14	chr12:42984600-42985000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
15	chr12:42984600-42985000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
16	chr12:42984600-42985000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:42984600-42985000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
18	chr12:42984600-42985000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
19	chr12:42984600-42985000	Flanking Active TSS	Fetal Heart	heart
20	chr12:42984600-42985200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
21	chr12:42984600-42987000	Weak transcription	Stomach Mucosa	stomach
22	chr12:42984800-42985000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr12:42984800-42985000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:42984800-42985000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:42984800-42985000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:42984800-42985000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:42984800-42985000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:42984800-42985000	Enhancers	Adipose Nuclei	Adipose
29	chr12:42984800-42985000	Active TSS	Brain Angular Gyrus	brain
30	chr12:42984800-42985000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr12:42984800-42985000	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr12:42984800-42985000	Active TSS	Stomach Smooth Muscle	stomach
33	chr12:42984800-42985000	Enhancers	HSMMtube	muscle
34	chr12:42984800-42985000	Flanking Active TSS	NH-A	brain
35	chr12:42984800-42985200	Bivalent Enhancer	Primary hematopoietic stem cells	blood

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