Variant report

Variant	rs856058
Chromosome Location	chr1:159002155-159002156
allele	A/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	POLR2A	chr1:159000061-159007717	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
IFI16	TF binding region

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1057027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1057028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1101991	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1101993	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs1101994	0.95[ASN][1000 genomes]
rs1101995	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.95[ASN][1000 genomes]
rs1101996	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs1101998	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs11265131	1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[ASN][1000 genomes]
rs11265132	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11265133	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12061402	0.89[ASN][1000 genomes]
rs12087333	0.95[ASN][1000 genomes]
rs12090965	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12093523	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12094545	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12094692	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12094741	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12094786	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12120311	0.94[ASN][1000 genomes]
rs12124059	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12139793	0.95[ASN][1000 genomes]
rs12144575	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12239136	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12240111	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1417804	0.89[EUR][1000 genomes]
rs1614182	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1633256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1633262	0.90[EUR][1000 genomes]
rs1633265	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs16841532	0.87[YRI][hapmap]
rs1772405	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs1772408	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1772414	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1772415	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2106094	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2106095	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2157694	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2157695	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2239890	0.95[ASN][1000 genomes]
rs2518553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2570916	1.00[CEU][hapmap]
rs2840312	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4531291	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4575082	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55853408	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56235865	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56248786	0.95[ASN][1000 genomes]
rs56348543	0.95[ASN][1000 genomes]
rs56374780	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60958912	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66831955	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67772786	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67843408	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73021886	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74122214	1.00[ASN][1000 genomes]
rs7525853	0.95[ASN][1000 genomes]
rs7535630	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7535856	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs7538035	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7540687	0.95[ASN][1000 genomes]
rs7545770	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs855865	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs855866	0.84[CEU][hapmap]
rs856050	0.95[ASN][1000 genomes]
rs856051	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856054	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs856055	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs856057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs861318	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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
3	esv2323695	chr1:159002155-159002156	Strong transcription Weak transcription Genic enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs856058	AIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:158982600-159027400	Weak transcription	Fetal Kidney	kidney
3	chr1:158984200-159024200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:158984800-159027400	Weak transcription	Psoas Muscle	Psoas
5	chr1:158985400-159023800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:158985800-159005000	Weak transcription	Brain Angular Gyrus	brain
7	chr1:158986000-159016200	Weak transcription	Stomach Mucosa	stomach
8	chr1:158988000-159002200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:158988200-159016600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:158988400-159002400	Weak transcription	Fetal Brain Male	brain
11	chr1:158988600-159024000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr1:158989000-159002400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:158989000-159003000	Weak transcription	Colonic Mucosa	Colon
14	chr1:158989800-159004200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr1:158993000-159023200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:158996400-159009800	Strong transcription	GM12878-XiMat	blood
17	chr1:158997600-159017000	Strong transcription	Primary B cells from cord blood	blood
18	chr1:158998400-159008400	Strong transcription	HSMM	muscle
19	chr1:158998400-159008400	Strong transcription	Osteobl	bone
20	chr1:158998400-159008800	Strong transcription	Muscle Satellite Cultured Cells	--
21	chr1:158998400-159024000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr1:158998600-159014600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:158998600-159015600	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:158998800-159014000	Strong transcription	Primary T cells from cord blood	blood
25	chr1:158998800-159033800	Weak transcription	Fetal Brain Female	brain
26	chr1:158999000-159014400	Strong transcription	Fetal Intestine Large	intestine
27	chr1:158999000-159022800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr1:158999200-159023800	Strong transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:158999400-159013000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:158999600-159007200	Strong transcription	Fetal Lung	lung
31	chr1:158999600-159013000	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr1:158999800-159002400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:158999800-159002600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr1:158999800-159007600	Strong transcription	Brain Hippocampus Middle	brain
35	chr1:159000000-159004800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
36	chr1:159000000-159005200	Strong transcription	Fetal Muscle Leg	muscle
37	chr1:159000000-159008800	Strong transcription	HSMMtube	muscle
38	chr1:159000000-159009000	Strong transcription	Placenta	Placenta
39	chr1:159000000-159012800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr1:159000000-159012800	Strong transcription	NHEK	skin
41	chr1:159000000-159026200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:159000200-159002600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:159000200-159003200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:159000200-159003400	Strong transcription	Brain Substantia Nigra	brain
45	chr1:159000200-159009000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:159000200-159009200	Strong transcription	Hela-S3	cervix
47	chr1:159000200-159010000	Strong transcription	Liver	Liver
48	chr1:159000200-159011800	Strong transcription	Rectal Mucosa Donor 31	rectum
49	chr1:159000200-159013200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr1:159000200-159013400	Strong transcription	Thymus	Thymus

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