Variant report

Variant	rs12059564
Chromosome Location	chr1:159000779-159000780
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	EBF1	chr1:159000571-159001014	GM12878	blood:	n/a	chr1:159000846-159000857
2	YY1	chr1:159000743-159001115	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:159000061-159007717	GM12891	blood:	n/a	n/a
4	POLR2A	chr1:159000626-159000990	U87	brain:	n/a	n/a
5	EBF1	chr1:159000618-159001442	GM12878	blood:	n/a	chr1:159000846-159000857
6	CTCF	chr1:159000738-159000792	GM13977	blood:	n/a	n/a
7	POLR2A	chr1:159000623-159001239	GM12878	blood:	n/a	n/a
8	EBF1	chr1:159000621-159001040	GM12878	blood:	n/a	chr1:159000846-159000857
9	POLR2A	chr1:159000688-159001074	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:159000767-159000839	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr1:159000626-159000999	U87	brain:	n/a	n/a

Variant related genes	Relation type
IFI16	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1057024	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10908699	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1101988	0.92[ASN][1000 genomes]
rs1101997	0.94[ASN][1000 genomes]
rs74122213	0.88[EUR][1000 genomes]
rs856043	0.89[ASN][1000 genomes]
rs856044	0.93[ASN][1000 genomes]
rs856046	0.84[ASN][1000 genomes]
rs856049	0.95[ASN][1000 genomes]
rs856054	0.96[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	esv3369957	chr1:158915589-159003393	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv872486	chr1:158979191-159090256	Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12059564	AIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158976000-159000800	Weak transcription	Gastric	stomach
2	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:158982600-159027400	Weak transcription	Fetal Kidney	kidney
4	chr1:158984000-159000800	Weak transcription	Right Ventricle	heart
5	chr1:158984200-159024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:158984800-159027400	Weak transcription	Psoas Muscle	Psoas
7	chr1:158985400-159023800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:158985800-159005000	Weak transcription	Brain Angular Gyrus	brain
9	chr1:158986000-159016200	Weak transcription	Stomach Mucosa	stomach
10	chr1:158987200-159001200	Strong transcription	Fetal Thymus	thymus
11	chr1:158988000-159002200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr1:158988200-159016600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:158988400-159002400	Weak transcription	Fetal Brain Male	brain
14	chr1:158988600-159024000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:158988800-159000800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr1:158989000-159002400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:158989000-159003000	Weak transcription	Colonic Mucosa	Colon
18	chr1:158989800-159004200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:158993000-159023200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:158993800-159002000	Weak transcription	NH-A	brain
21	chr1:158994000-159000800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr1:158996400-159009800	Strong transcription	GM12878-XiMat	blood
23	chr1:158997600-159017000	Strong transcription	Primary B cells from cord blood	blood
24	chr1:158998400-159001400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr1:158998400-159008400	Strong transcription	HSMM	muscle
26	chr1:158998400-159008400	Strong transcription	Osteobl	bone
27	chr1:158998400-159008800	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr1:158998400-159024000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:158998600-159014600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr1:158998600-159015600	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:158998800-159001000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr1:158998800-159014000	Strong transcription	Primary T cells from cord blood	blood
33	chr1:158998800-159033800	Weak transcription	Fetal Brain Female	brain
34	chr1:158999000-159000800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr1:158999000-159014400	Strong transcription	Fetal Intestine Large	intestine
36	chr1:158999000-159022800	Strong transcription	Primary neutrophils fromperipheralblood	blood
37	chr1:158999200-159000800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr1:158999200-159001800	Weak transcription	Rectal Smooth Muscle	rectum
39	chr1:158999200-159023800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr1:158999400-159001600	Strong transcription	Fetal Stomach	stomach
41	chr1:158999400-159013000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:158999600-159007200	Strong transcription	Fetal Lung	lung
43	chr1:158999600-159013000	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:158999800-159000800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr1:158999800-159002400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:158999800-159002600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:158999800-159007600	Strong transcription	Brain Hippocampus Middle	brain
48	chr1:159000000-159001200	Genic enhancers	HUVEC	blood vessel
49	chr1:159000000-159001400	Genic enhancers	Adipose Nuclei	Adipose
50	chr1:159000000-159001400	Strong transcription	Small Intestine	intestine

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