Variant report

Variant	rs12822085
Chromosome Location	chr12:48588782-48588783
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	ATF1	chr12:48588773-48588802	K562	blood:	n/a	n/a
2	TCF12	chr12:48588191-48589362	SK-N-SH	brain:	n/a	n/a
3	FOSL2	chr12:48588463-48589244	SK-N-SH	brain:	n/a	n/a
4	JUND	chr12:48588382-48589138	SK-N-SH	brain:	n/a	n/a
5	GATA2	chr12:48588487-48589160	SH-SY5Y	brain:	n/a	chr12:48588541-48588551 chr12:48588528-48588541 chr12:48588532-48588543
6	MEF2A	chr12:48588405-48589079	SK-N-SH	brain:	n/a	chr12:48588543-48588551 chr12:48588556-48588571 chr12:48588480-48588497
7	TEAD4	chr12:48588390-48589309	SK-N-SH	brain:	n/a	n/a
8	PBX3	chr12:48588347-48589056	SK-N-SH	brain:	n/a	n/a
9	TEAD4	chr12:48588417-48589092	SK-N-SH	brain:	n/a	n/a
10	GATA3	chr12:48588138-48589217	SH-SY5Y	brain:	n/a	chr12:48588541-48588551 chr12:48588528-48588541 chr12:48588532-48588543
11	EP300	chr12:48588174-48589543	SK-N-SH	brain:	n/a	n/a
12	PBX3	chr12:48588348-48589302	SK-N-SH	brain:	n/a	n/a
13	EP300	chr12:48588431-48588900	SK-N-SH_RA	brain:	n/a	n/a
14	TCF12	chr12:48588221-48589384	SK-N-SH	brain:	n/a	n/a
15	GATA3	chr12:48588286-48589380	SK-N-SH	brain:	n/a	chr12:48588541-48588551 chr12:48588528-48588541 chr12:48588532-48588543
16	EP300	chr12:48588495-48588888	SK-N-SH_RA	brain:	n/a	n/a
17	POLR2A	chr12:48588492-48589077	SK-N-SH	brain:	n/a	n/a
18	EP300	chr12:48588404-48589312	SK-N-SH	brain:	n/a	n/a
19	PRDM1	chr12:48588610-48588961	Hela-S3	cervix:	n/a	n/a
20	GATA3	chr12:48588189-48589414	SK-N-SH	brain:	n/a	chr12:48588541-48588551 chr12:48588528-48588541 chr12:48588532-48588543
21	JUND	chr12:48588311-48589261	SK-N-SH	brain:	n/a	n/a
22	NFIC	chr12:48588234-48589244	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48587647..48589983-chr12:48590622..48592534,2	K562	blood:
2	chr12:48582939..48584871-chr12:48586838..48589561,2	K562	blood:

Variant related genes	Relation type
ENSG00000269514	TF binding region
ENSG00000269514	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1018973	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs10492080	1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1074174	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10783231	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.96[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783232	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10783233	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10783237	0.81[ASN][1000 genomes]
rs11168449	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168451	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168455	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11609399	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11612578	0.95[JPT][hapmap]
rs11613485	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs1476608	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs1489111	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs17122565	0.92[GIH][hapmap];0.95[JPT][hapmap];0.81[TSI][hapmap]
rs17122612	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs17122651	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap]
rs1968071	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs2054902	0.84[GIH][hapmap];0.81[JPT][hapmap]
rs2258342	0.85[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs2409001	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2634679	0.84[GIH][hapmap];0.81[JPT][hapmap]
rs2634699	0.95[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap]
rs2732455	0.85[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs2732477	0.85[CHB][hapmap];0.84[GIH][hapmap];0.81[JPT][hapmap]
rs2732487	0.85[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap]
rs3742074	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs4075913	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4141065	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4760611	0.89[GIH][hapmap];0.95[JPT][hapmap]
rs4760620	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4760683	0.81[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap]
rs4760685	0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4760692	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4760698	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6580653	0.88[ASN][1000 genomes]
rs6580656	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6580657	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6580660	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs726354	1.00[CHB][hapmap];0.83[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs7294641	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7296913	0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap]
rs7305418	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7312326	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs7313023	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7315258	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7485057	0.88[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7485824	0.88[ASN][1000 genomes]
rs757556	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7963934	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7969749	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7971668	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs879242	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs901962	0.84[GIH][hapmap];0.81[JPT][hapmap]
rs901963	0.82[GIH][hapmap];0.81[JPT][hapmap]
rs901964	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv33956	chr12:48565643-48645561	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12822085	ZNF641	cis	Muscle Skeletal	GTEx
rs12822085	ZNF641	cis	multi-tissue	Pritchard
rs12822085	ZNF641	cis	Whole Blood	GTEx
rs12822085	H1T2	cis	multi-tissue	Pritchard

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48580000-48591000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr12:48583000-48590200	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr12:48585400-48590800	Weak transcription	HMEC	breast
4	chr12:48585800-48589800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:48585800-48591400	Weak transcription	Esophagus	oesophagus
6	chr12:48587400-48589200	Enhancers	Hela-S3	cervix
7	chr12:48587400-48590600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr12:48587400-48590800	Weak transcription	NHEK	skin
9	chr12:48587600-48590800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:48588000-48589400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:48588200-48588800	Bivalent Enhancer	HUVEC	blood vessel
12	chr12:48588200-48589200	Bivalent Enhancer	Osteobl	bone
13	chr12:48588200-48590000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:48588400-48589200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:48588400-48589400	Weak transcription	Placenta	Placenta
16	chr12:48588400-48590000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr12:48588400-48590800	Enhancers	A549	lung
18	chr12:48588600-48588800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr12:48588600-48588800	Enhancers	Fetal Kidney	kidney
20	chr12:48588600-48589000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:48588600-48589200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:48588600-48589200	Enhancers	Fetal Heart	heart

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