Variant report

Variant	rs856054
Chromosome Location	chr1:159001521-159001522
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	POLR2A	chr1:159000061-159007717	GM12891	blood:	n/a	n/a

Variant related genes	Relation type
IFI16	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1057024	0.88[CHB][hapmap];0.94[ASN][1000 genomes]
rs1057027	0.91[CEU][hapmap];0.89[CHB][hapmap]
rs1057028	0.91[CEU][hapmap];0.89[CHB][hapmap]
rs10908699	0.94[ASN][1000 genomes]
rs1101988	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1101991	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs1101993	0.93[CEU][hapmap];0.89[CHB][hapmap];0.89[EUR][1000 genomes]
rs1101994	0.89[EUR][1000 genomes]
rs1101995	1.00[CEU][hapmap];0.88[CHB][hapmap];0.89[EUR][1000 genomes]
rs1101996	0.85[CEU][hapmap];0.89[CHB][hapmap];0.89[EUR][1000 genomes]
rs1101997	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1101998	0.91[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes]
rs11265131	0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs11265133	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs12059564	0.96[ASN][1000 genomes]
rs12087333	0.89[EUR][1000 genomes]
rs12093523	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs12094741	0.91[CEU][hapmap];0.89[CHB][hapmap]
rs12098223	0.82[CEU][hapmap]
rs12120311	0.89[EUR][1000 genomes]
rs12124059	0.90[CEU][hapmap]
rs12139793	0.89[EUR][1000 genomes]
rs1417804	0.83[EUR][1000 genomes]
rs1614182	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs1633256	0.91[CEU][hapmap];0.89[CHB][hapmap]
rs1633262	0.85[EUR][1000 genomes]
rs1633265	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs1772405	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs1772407	0.82[CEU][hapmap]
rs1772408	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs1772414	0.91[CEU][hapmap];0.84[CHB][hapmap]
rs1772415	0.91[CEU][hapmap];0.84[CHB][hapmap]
rs2106095	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs2570916	0.91[CEU][hapmap];1.00[YRI][hapmap]
rs2814770	0.82[CEU][hapmap]
rs2814771	0.82[CEU][hapmap]
rs3018316	0.83[CEU][hapmap]
rs3737522	0.82[CEU][hapmap]
rs3754460	0.82[CEU][hapmap]
rs3768513	0.82[CEU][hapmap]
rs56248786	0.89[EUR][1000 genomes]
rs56348543	0.89[EUR][1000 genomes]
rs7525853	0.89[EUR][1000 genomes]
rs7535856	0.89[CHB][hapmap];0.80[EUR][1000 genomes]
rs7540687	0.89[EUR][1000 genomes]
rs855865	0.91[CEU][hapmap]
rs855866	1.00[YRI][hapmap]
rs856043	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs856044	0.91[ASN][1000 genomes]
rs856046	0.80[CHB][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs856049	0.94[CHB][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs856052	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs856053	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs856055	0.90[CHB][hapmap]
rs856058	0.93[CEU][hapmap];0.90[CHB][hapmap]
rs861318	0.91[CEU][hapmap];0.84[CHB][hapmap]

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
rs856054	AIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:103 , 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	chr1:158993800-159002000	Weak transcription	NH-A	brain
17	chr1:158996400-159009800	Strong transcription	GM12878-XiMat	blood
18	chr1:158997600-159017000	Strong transcription	Primary B cells from cord blood	blood
19	chr1:158998400-159008400	Strong transcription	HSMM	muscle
20	chr1:158998400-159008400	Strong transcription	Osteobl	bone
21	chr1:158998400-159008800	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr1:158998400-159024000	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr1:158998600-159014600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr1:158998600-159015600	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr1:158998800-159014000	Strong transcription	Primary T cells from cord blood	blood
26	chr1:158998800-159033800	Weak transcription	Fetal Brain Female	brain
27	chr1:158999000-159014400	Strong transcription	Fetal Intestine Large	intestine
28	chr1:158999000-159022800	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr1:158999200-159001800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:158999200-159023800	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr1:158999400-159001600	Strong transcription	Fetal Stomach	stomach
32	chr1:158999400-159013000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr1:158999600-159007200	Strong transcription	Fetal Lung	lung
34	chr1:158999600-159013000	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:158999800-159002400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:158999800-159002600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr1:158999800-159007600	Strong transcription	Brain Hippocampus Middle	brain
38	chr1:159000000-159004800	Strong transcription	Primary T killer memory cells from peripheral blood	blood
39	chr1:159000000-159005200	Strong transcription	Fetal Muscle Leg	muscle
40	chr1:159000000-159008800	Strong transcription	HSMMtube	muscle
41	chr1:159000000-159009000	Strong transcription	Placenta	Placenta
42	chr1:159000000-159012800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:159000000-159012800	Strong transcription	NHEK	skin
44	chr1:159000000-159026200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr1:159000200-159001800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:159000200-159002600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:159000200-159003200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:159000200-159003400	Strong transcription	Brain Substantia Nigra	brain
49	chr1:159000200-159009000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr1:159000200-159009200	Strong transcription	Hela-S3	cervix

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