Variant report

Variant	rs2840312
Chromosome Location	chr1:159000027-159000028
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	SETDB1	chr1:158999712-159000142	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
IFI16	TF binding region

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1057027	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1057028	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1101991	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1101993	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1101994	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1101995	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1101996	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1101998	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265131	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11265132	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265133	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12061402	0.91[ASN][1000 genomes]
rs12087333	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12090965	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12093523	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12094545	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12094692	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12094741	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12094786	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12120311	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124059	0.83[EUR][1000 genomes]
rs12139793	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12144575	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12239136	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12240111	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1417804	0.82[EUR][1000 genomes]
rs1614182	0.84[EUR][1000 genomes]
rs1633256	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1633262	0.84[EUR][1000 genomes]
rs1633265	0.84[EUR][1000 genomes]
rs1772405	0.84[EUR][1000 genomes]
rs1772408	0.83[EUR][1000 genomes]
rs1772414	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1772415	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2106094	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2106095	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2157694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2157695	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239890	0.98[ASN][1000 genomes]
rs2518553	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4531291	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4575082	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55853408	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56235865	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56248786	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56348543	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56374780	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60958912	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66831955	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67772786	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67843408	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73021886	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74122214	0.94[ASN][1000 genomes]
rs7525853	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7535630	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7535856	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs7538035	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7540687	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7545770	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs855865	0.82[EUR][1000 genomes]
rs856050	0.98[ASN][1000 genomes]
rs856051	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs856052	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs856053	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs856055	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs856056	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs856057	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs856058	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs861318	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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
rs2840312	AIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

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	chr1:158982800-159000200	Weak transcription	Aorta	Aorta
5	chr1:158984000-159000800	Weak transcription	Right Ventricle	heart
6	chr1:158984200-159024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:158984800-159027400	Weak transcription	Psoas Muscle	Psoas
8	chr1:158985400-159023800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:158985800-159005000	Weak transcription	Brain Angular Gyrus	brain
10	chr1:158986000-159016200	Weak transcription	Stomach Mucosa	stomach
11	chr1:158987000-159000200	Weak transcription	Brain Substantia Nigra	brain
12	chr1:158987000-159000400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:158987200-159000200	Weak transcription	Stomach Smooth Muscle	stomach
14	chr1:158987200-159000400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:158987200-159001200	Strong transcription	Fetal Thymus	thymus
16	chr1:158987800-159000200	Weak transcription	Esophagus	oesophagus
17	chr1:158988000-159002200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr1:158988200-159000200	Weak transcription	Left Ventricle	heart
19	chr1:158988200-159016600	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:158988400-159002400	Weak transcription	Fetal Brain Male	brain
21	chr1:158988600-159024000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr1:158988800-159000800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:158989000-159002400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:158989000-159003000	Weak transcription	Colonic Mucosa	Colon
25	chr1:158989800-159004200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:158990200-159000200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:158991600-159000200	Weak transcription	Liver	Liver
28	chr1:158991600-159000200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:158991600-159000200	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr1:158991600-159000400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr1:158992400-159000200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:158993000-159023200	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr1:158993800-159000600	Weak transcription	HMEC	breast
34	chr1:158993800-159002000	Weak transcription	NH-A	brain
35	chr1:158994000-159000200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:158994000-159000800	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:158994400-159000200	Weak transcription	Spleen	Spleen
38	chr1:158994400-159000400	Weak transcription	Colon Smooth Muscle	Colon
39	chr1:158994400-159000400	Weak transcription	NHDF-Ad	bronchial
40	chr1:158994600-159000200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:158994600-159000200	Weak transcription	Hela-S3	cervix
42	chr1:158995000-159000200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr1:158995200-159000200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:158995200-159000200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:158995200-159000200	Weak transcription	Lung	lung
46	chr1:158995200-159000200	Weak transcription	Ovary	ovary
47	chr1:158995200-159000200	Weak transcription	Thymus	Thymus
48	chr1:158995200-159000200	Weak transcription	NHLF	lung
49	chr1:158996400-159009800	Strong transcription	GM12878-XiMat	blood
50	chr1:158996600-159000200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links