Variant report

Variant	rs1796390
Chromosome Location	chr12:42878604-42878605
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	MAX	chr12:42876530-42878610	ECC-1	luminal epithelium:	n/a	n/a
2	TBP	chr12:42877310-42878710	H1-hESC	embryonic stem cell:	n/a	n/a
3	SETDB1	chr12:42878329-42879489	U2OS	brain:	n/a	n/a
4	RCOR1	chr12:42878372-42878617	GM12878	blood:	n/a	n/a
5	ZNF384	chr12:42877276-42879284	K562	blood:	n/a	n/a
6	KAP1	chr12:42877878-42879180	HEK293	kidney:	n/a	n/a
7	MAZ	chr12:42875835-42878737	IMR90	lung:	n/a	n/a
8	TCF7L2	chr12:42877380-42878957	HEK293	kidney:	n/a	n/a
9	JUND	chr12:42877887-42878806	H1-hESC	embryonic stem cell:	n/a	chr12:42878077-42878086
10	RAD21	chr12:42875639-42878864	SK-N-SH	brain:	n/a	chr12:42876704-42876716 chr12:42876757-42876776 chr12:42877771-42877784 chr12:42876706-42876716 chr12:42877442-42877456 chr12:42876360-42876373
11	SIN3A	chr12:42875185-42878606	H1-hESC	embryonic stem cell:	n/a	chr12:42877917-42877930 chr12:42877519-42877532 chr12:42877448-42877461 chr12:42877569-42877580 chr12:42877192-42877203 chr12:42877183-42877196
12	KAP1	chr12:42877979-42879209	U2OS	brain:	n/a	n/a
13	CTCF	chr12:42876182-42878695	A549	lung:	n/a	chr12:42877455-42877468 chr12:42876756-42876774 chr12:42876757-42876773 chr12:42876759-42876772 chr12:42877770-42877783 chr12:42877909-42877922 chr12:42876707-42876717 chr12:42877428-42877441 chr12:42877130-42877143 chr12:42876733-42876746 chr12:42877429-42877439 chr12:42877378-42877391
14	MXI1	chr12:42876415-42879515	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
PRICKLE1	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11181522	0.88[EUR][1000 genomes]
rs1669915	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1669916	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669917	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669921	1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1669926	0.96[EUR][1000 genomes]
rs1669927	0.97[EUR][1000 genomes]
rs1669929	0.95[CEU][hapmap];0.89[GIH][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1796361	1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796362	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796391	1.00[CEU][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2708068	1.00[CEU][hapmap];0.94[GIH][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42875400-42878800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr12:42875400-42878800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr12:42875400-42878800	Active TSS	NHLF	lung
4	chr12:42876400-42878800	Active TSS	Stomach Smooth Muscle	stomach
5	chr12:42877200-42878800	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr12:42878200-42878800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:42878200-42878800	Flanking Active TSS	Fetal Heart	heart
8	chr12:42878200-42879000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:42878200-42879400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:42878200-42879400	Flanking Active TSS	HUVEC	blood vessel
11	chr12:42878200-42879800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr12:42878200-42879800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr12:42878200-42881000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:42878200-42882000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:42878200-42882800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:42878200-42883600	Weak transcription	Lung	lung
17	chr12:42878200-42884400	Weak transcription	Gastric	stomach
18	chr12:42878200-42885200	Weak transcription	Spleen	Spleen
19	chr12:42878400-42878800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr12:42878400-42878800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr12:42878400-42878800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
22	chr12:42878400-42878800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:42878400-42878800	Flanking Active TSS	Fetal Kidney	kidney
24	chr12:42878400-42879000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:42878400-42879000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:42878400-42879000	Enhancers	HSMM	muscle
27	chr12:42878400-42879800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
28	chr12:42878400-42879800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
29	chr12:42878400-42881200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:42878400-42883600	Weak transcription	Left Ventricle	heart
31	chr12:42878400-42888800	Weak transcription	Fetal Muscle Leg	muscle
32	chr12:42878600-42878800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr12:42878600-42878800	Enhancers	Primary B cells from peripheral blood	blood
34	chr12:42878600-42878800	Enhancers	Rectal Smooth Muscle	rectum
35	chr12:42878600-42878800	Bivalent/Poised TSS	GM12878-XiMat	blood
36	chr12:42878600-42878800	Enhancers	HSMMtube	muscle
37	chr12:42878600-42878800	Enhancers	NHEK	skin
38	chr12:42878600-42879000	Active TSS	H1 Cell Line	embryonic stem cell
39	chr12:42878600-42879000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr12:42878600-42879000	Enhancers	HMEC	breast
41	chr12:42878600-42879000	Enhancers	NH-A	brain
42	chr12:42878600-42879000	Enhancers	Osteobl	bone
43	chr12:42878600-42879200	Enhancers	Primary B cells from cord blood	blood
44	chr12:42878600-42879200	Enhancers	Fetal Stomach	stomach
45	chr12:42878600-42879400	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr12:42878600-42879600	Weak transcription	Brain Angular Gyrus	brain
47	chr12:42878600-42879600	Weak transcription	Ovary	ovary
48	chr12:42878600-42879800	Weak transcription	K562	blood
49	chr12:42878600-42880000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr12:42878600-42881000	Enhancers	Fetal Lung	lung

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