Variant report

Variant	rs3747565
Chromosome Location	chr12:42879260-42879261
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	SETDB1	chr12:42878329-42879489	U2OS	brain:	n/a	n/a
2	ZNF384	chr12:42877276-42879284	K562	blood:	n/a	n/a
3	CHD1	chr12:42879183-42879768	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZNF384	chr12:42878779-42879268	GM12878	blood:	n/a	n/a
5	MXI1	chr12:42876415-42879515	SK-N-SH	brain:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZCRB1-1	chr12:42879155-42879304	ENSG00000258068.1

Variant related genes	Relation type
PRICKLE1	TF binding region

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs11181518	0.86[EUR][1000 genomes]
rs11181519	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370828	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3747564	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];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	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

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42878200-42879400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:42878200-42879400	Flanking Active TSS	HUVEC	blood vessel
3	chr12:42878200-42879800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr12:42878200-42879800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr12:42878200-42881000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:42878200-42882000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:42878200-42882800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:42878200-42883600	Weak transcription	Lung	lung
9	chr12:42878200-42884400	Weak transcription	Gastric	stomach
10	chr12:42878200-42885200	Weak transcription	Spleen	Spleen
11	chr12:42878400-42879800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr12:42878400-42879800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
13	chr12:42878400-42881200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:42878400-42883600	Weak transcription	Left Ventricle	heart
15	chr12:42878400-42888800	Weak transcription	Fetal Muscle Leg	muscle
16	chr12:42878600-42879400	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr12:42878600-42879600	Weak transcription	Brain Angular Gyrus	brain
18	chr12:42878600-42879600	Weak transcription	Ovary	ovary
19	chr12:42878600-42879800	Weak transcription	K562	blood
20	chr12:42878600-42880000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:42878600-42881000	Enhancers	Fetal Lung	lung
22	chr12:42878600-42884400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr12:42878600-42889000	Weak transcription	Fetal Muscle Trunk	muscle
24	chr12:42878600-42892600	Weak transcription	Right Ventricle	heart
25	chr12:42878600-42904800	Weak transcription	Right Atrium	heart
26	chr12:42878800-42879400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr12:42878800-42879600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:42878800-42880600	Enhancers	Fetal Heart	heart
29	chr12:42878800-42896400	Weak transcription	Fetal Kidney	kidney
30	chr12:42878800-42898000	Weak transcription	HSMMtube	muscle
31	chr12:42878800-42902000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:42879000-42880200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:42879000-42880400	Enhancers	H1 Cell Line	embryonic stem cell
34	chr12:42879000-42881200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr12:42879000-42881400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr12:42879000-42887600	Weak transcription	Osteobl	bone
37	chr12:42879000-42898000	Weak transcription	NH-A	brain
38	chr12:42879000-42901000	Weak transcription	HSMM	muscle
39	chr12:42879200-42879800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr12:42879200-42879800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr12:42879200-42888800	Weak transcription	Fetal Stomach	stomach

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