Variant report

Variant	rs1669916
Chromosome Location	chr12:42878879-42878880
allele	G/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	SIN3A	chr12:42878866-42879149	H1-hESC	embryonic stem cell:	n/a	n/a
2	SETDB1	chr12:42878329-42879489	U2OS	brain:	n/a	n/a
3	ZNF384	chr12:42877276-42879284	K562	blood:	n/a	n/a
4	MEF2A	chr12:42878754-42879162	K562	blood:	n/a	chr12:42878962-42878976 chr12:42878961-42878976 chr12:42878957-42878978 chr12:42878957-42878978 chr12:42878939-42878954 chr12:42878963-42878974 chr12:42878964-42878973
5	MEF2C	chr12:42878733-42879073	GM12878	blood:	n/a	chr12:42878962-42878976 chr12:42878938-42878953 chr12:42878957-42878978 chr12:42878957-42878978 chr12:42878963-42878974 chr12:42878964-42878973
6	KAP1	chr12:42877878-42879180	HEK293	kidney:	n/a	n/a
7	BHLHE40	chr12:42878803-42879109	K562	blood:	n/a	n/a
8	TCF7L2	chr12:42877380-42878957	HEK293	kidney:	n/a	n/a
9	MEF2A	chr12:42878788-42879117	GM12878	blood:	n/a	chr12:42878962-42878976 chr12:42878961-42878976 chr12:42878957-42878978 chr12:42878957-42878978 chr12:42878939-42878954 chr12:42878963-42878974 chr12:42878964-42878973
10	ZNF384	chr12:42878779-42879268	GM12878	blood:	n/a	n/a
11	RCOR1	chr12:42878835-42879125	K562	blood:	n/a	n/a
12	KAP1	chr12:42877979-42879209	U2OS	brain:	n/a	n/a
13	MEF2A	chr12:42878789-42879157	K562	blood:	n/a	chr12:42878962-42878976 chr12:42878961-42878976 chr12:42878957-42878978 chr12:42878957-42878978 chr12:42878939-42878954 chr12:42878963-42878974 chr12:42878964-42878973
14	MEF2A	chr12:42878754-42879095	GM12878	blood:	n/a	chr12:42878962-42878976 chr12:42878961-42878976 chr12:42878957-42878978 chr12:42878957-42878978 chr12:42878939-42878954 chr12:42878963-42878974 chr12:42878964-42878973
15	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: 16 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11181522	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1669915	0.94[EUR][1000 genomes]
rs1669917	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669921	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1669926	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1669927	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1669929	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1796361	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1796362	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1796364	0.82[ASN][1000 genomes]
rs1796390	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1796391	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2708068	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:45 , 50 per page) page: 1

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

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