Variant report

Variant	rs1772408
Chromosome Location	chr1:159005649-159005650
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1057027	1.00[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs1057028	1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs1101991	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs1101993	0.82[CEU][hapmap]
rs1101995	0.81[CEU][hapmap]
rs1101998	0.82[CEU][hapmap];0.94[GIH][hapmap]
rs11265132	0.83[EUR][1000 genomes]
rs11265133	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs12090965	0.83[EUR][1000 genomes]
rs12093523	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs12094545	0.83[EUR][1000 genomes]
rs12094692	0.83[EUR][1000 genomes]
rs12094741	0.82[CEU][hapmap];0.92[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs12094786	0.83[EUR][1000 genomes]
rs12098223	0.86[GIH][hapmap]
rs12124059	1.00[CEU][hapmap];0.88[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs12144575	0.83[EUR][1000 genomes]
rs12239136	0.83[EUR][1000 genomes]
rs12240111	0.83[EUR][1000 genomes]
rs1417804	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1614182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1616024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[ASN][1000 genomes]
rs1633256	1.00[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs1633262	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633266	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1633267	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1772405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1772407	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1772414	1.00[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs1772415	1.00[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs2106094	0.83[EUR][1000 genomes]
rs2106095	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs2157694	0.83[EUR][1000 genomes]
rs2157695	0.83[EUR][1000 genomes]
rs2518553	0.89[EUR][1000 genomes]
rs2570916	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap]
rs2814770	0.82[GIH][hapmap]
rs2814771	0.83[GIH][hapmap]
rs2840312	0.83[EUR][1000 genomes]
rs2852699	0.92[ASN][1000 genomes]
rs3737522	0.86[GIH][hapmap]
rs3754460	0.86[GIH][hapmap]
rs3768513	0.86[GIH][hapmap]
rs56235865	0.83[EUR][1000 genomes]
rs56374780	0.83[EUR][1000 genomes]
rs60958912	0.83[EUR][1000 genomes]
rs66831955	0.83[EUR][1000 genomes]
rs67772786	0.83[EUR][1000 genomes]
rs67843408	0.83[EUR][1000 genomes]
rs73021886	0.83[EUR][1000 genomes]
rs7535630	0.83[EUR][1000 genomes]
rs7535856	0.89[GIH][hapmap]
rs7538035	0.83[EUR][1000 genomes]
rs7545770	0.83[EUR][1000 genomes]
rs855865	1.00[CEU][hapmap];0.91[GIH][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs855866	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs855867	0.85[CHD][hapmap]
rs855871	0.91[CHD][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap]
rs856051	0.82[EUR][1000 genomes]
rs856052	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs856053	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs856054	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs856055	0.93[CEU][hapmap];0.94[GIH][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs856056	0.89[EUR][1000 genomes]
rs856057	0.89[EUR][1000 genomes]
rs856058	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs861318	1.00[CEU][hapmap];0.94[GIH][hapmap];0.90[TSI][hapmap];0.89[EUR][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	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
2	esv3417048	chr1:159005419-159006183	Strong transcription Weak transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases
3	esv3438832	chr1:159005429-159006181	Strong transcription Weak transcription Genic enhancers	n/a	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Celiac disease or Rheumatoid arthritis	21383967	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1772408	AIM2	cis	lymphoblastoid	seeQTL
rs1772408	IFI16	cis	parietal	SCAN
rs1772408	CCDC19	cis	cerebellum	SCAN
rs1772408	AIM2	Cis_1M	lymphoblastoid	RTeQTL
rs1772408	IFI16	cis	cerebellum	SCAN
rs1772408	TMEM79	cis	parietal	SCAN
rs1772408	FCRL4	cis	cerebellum	SCAN

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

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	chr1:158986000-159016200	Weak transcription	Stomach Mucosa	stomach
7	chr1:158988200-159016600	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:158988600-159024000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:158993000-159023200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr1:158996400-159009800	Strong transcription	GM12878-XiMat	blood
11	chr1:158997600-159017000	Strong transcription	Primary B cells from cord blood	blood
12	chr1:158998400-159008400	Strong transcription	HSMM	muscle
13	chr1:158998400-159008400	Strong transcription	Osteobl	bone
14	chr1:158998400-159008800	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr1:158998400-159024000	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr1:158998600-159014600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr1:158998600-159015600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr1:158998800-159014000	Strong transcription	Primary T cells from cord blood	blood
19	chr1:158998800-159033800	Weak transcription	Fetal Brain Female	brain
20	chr1:158999000-159014400	Strong transcription	Fetal Intestine Large	intestine
21	chr1:158999000-159022800	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:158999200-159023800	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr1:158999400-159013000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr1:158999600-159007200	Strong transcription	Fetal Lung	lung
25	chr1:158999600-159013000	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:158999800-159007600	Strong transcription	Brain Hippocampus Middle	brain
27	chr1:159000000-159008800	Strong transcription	HSMMtube	muscle
28	chr1:159000000-159009000	Strong transcription	Placenta	Placenta
29	chr1:159000000-159012800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:159000000-159012800	Strong transcription	NHEK	skin
31	chr1:159000000-159026200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:159000200-159009000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr1:159000200-159009200	Strong transcription	Hela-S3	cervix
34	chr1:159000200-159010000	Strong transcription	Liver	Liver
35	chr1:159000200-159011800	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr1:159000200-159013200	Strong transcription	Primary hematopoietic stem cells	blood
37	chr1:159000200-159013400	Strong transcription	Thymus	Thymus
38	chr1:159000400-159014000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr1:159000400-159024200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr1:159000600-159007400	Strong transcription	HMEC	breast
41	chr1:159000600-159008600	Strong transcription	Dnd41	blood
42	chr1:159000600-159014200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:159000600-159020200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:159000600-159023800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr1:159000800-159008800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr1:159000800-159010800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr1:159001000-159007200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:159001000-159008600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:159001000-159008600	Strong transcription	NHDF-Ad	bronchial
50	chr1:159001000-159016000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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