Variant report

Variant	rs3759400
Chromosome Location	chr12:120104173-120104174
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	NFIC	chr12:120104029-120105869	GM12878	blood:	n/a	n/a
2	MAFF	chr12:120104096-120104366	HepG2	liver:	n/a	chr12:120104224-120104242
3	SPI1	chr12:120104086-120105263	GM12878	blood:	n/a	chr12:120104436-120104449 chr12:120104562-120104571 chr12:120104438-120104447
4	ZC3H11A	chr12:120104084-120104275	K562	blood:	n/a	n/a
5	EBF1	chr12:120104052-120105930	GM12878	blood:	n/a	n/a
6	IRF1	chr12:120103100-120104660	K562	blood:	n/a	n/a
7	MAFK	chr12:120104117-120104352	HepG2	liver:	n/a	chr12:120104225-120104240
8	MAFF	chr12:120103090-120104413	K562	blood:	n/a	chr12:120104224-120104242
9	MAFK	chr12:120104052-120104406	HepG2	liver:	n/a	chr12:120104225-120104240
10	RUNX3	chr12:120103990-120106155	GM12878	blood:	n/a	n/a
11	IRF1	chr12:120103209-120104319	K562	blood:	n/a	n/a
12	JUN	chr12:120102269-120104597	K562	blood:	n/a	chr12:120104564-120104573 chr12:120104405-120104414
13	MAFK	chr12:120104073-120104378	IMR90	lung:	n/a	chr12:120104225-120104240
14	MAFK	chr12:120103151-120104491	K562	blood:	n/a	chr12:120104225-120104240
15	CHD1	chr12:120104169-120106468	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:120103322..120105454-chr12:120505057..120506745,2	K562	blood:
2	chr12:119877799..119880484-chr12:120102287..120105032,2	K562	blood:
3	chr12:120085087..120087240-chr12:120102700..120105114,2	K562	blood:

Variant related genes	Relation type
PRKAB1	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11064888	0.81[ASN][1000 genomes]
rs1541345	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16949584	1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2285594	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs2519538	0.81[EUR][1000 genomes]
rs278121	1.00[CHB][hapmap]
rs35490437	0.88[ASN][1000 genomes]
rs4269	0.88[ASN][1000 genomes]
rs55775618	0.88[ASN][1000 genomes]
rs56096252	0.88[ASN][1000 genomes]
rs61068064	0.88[ASN][1000 genomes]
rs7297192	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7297487	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7308115	0.88[ASN][1000 genomes]
rs7309710	0.88[ASN][1000 genomes]
rs7311975	1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs73215355	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73221264	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73221268	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052595	chr12:119992580-120132038	Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv541616	chr12:119992580-120132038	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120100400-120105200	Weak transcription	Psoas Muscle	Psoas
2	chr12:120101800-120104800	Weak transcription	Right Ventricle	heart
3	chr12:120102200-120105200	Weak transcription	Aorta	Aorta
4	chr12:120102600-120104200	Enhancers	Thymus	Thymus
5	chr12:120102800-120104200	Weak transcription	HepG2	liver
6	chr12:120102800-120105000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr12:120103000-120104400	Flanking Active TSS	K562	blood
8	chr12:120103200-120104800	Enhancers	Fetal Thymus	thymus
9	chr12:120103400-120104200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr12:120103400-120104800	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr12:120103400-120104800	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr12:120103400-120104800	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr12:120103600-120104200	Enhancers	Primary T cells from cord blood	blood
14	chr12:120103600-120104200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr12:120103600-120104600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr12:120103600-120104800	Enhancers	Primary B cells from peripheral blood	blood
17	chr12:120103600-120104800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr12:120103600-120104800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:120103600-120104800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr12:120103600-120104800	Enhancers	Brain Angular Gyrus	brain
21	chr12:120103600-120105000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr12:120103600-120105000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr12:120103600-120105000	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr12:120103600-120105000	Enhancers	Adipose Nuclei	Adipose
25	chr12:120103600-120105400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:120103600-120105400	Flanking Active TSS	GM12878-XiMat	blood
27	chr12:120103800-120104200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr12:120103800-120104200	Enhancers	Dnd41	blood
29	chr12:120103800-120104400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:120103800-120104800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr12:120103800-120104800	Enhancers	Duodenum Mucosa	Duodenum
32	chr12:120103800-120105000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr12:120103800-120105200	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr12:120103800-120105400	Flanking Active TSS	Primary B cells from cord blood	blood
35	chr12:120103800-120105400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr12:120103800-120105600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
37	chr12:120104000-120104800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:120104000-120104800	Enhancers	Brain Anterior Caudate	brain
39	chr12:120104000-120104800	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:120104000-120104800	Enhancers	HUVEC	blood vessel
41	chr12:120104000-120105200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:120104000-120105200	Weak transcription	Placenta	Placenta
43	chr12:120104000-120105200	Weak transcription	Spleen	Spleen
44	chr12:120104000-120105400	Flanking Active TSS	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links