Variant report

Variant	rs3754460
Chromosome Location	chr1:159006846-159006847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1057027	0.82[CHD][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap]
rs1057028	0.82[CHD][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap]
rs1101998	0.85[GIH][hapmap]
rs11265134	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12094741	0.88[GIH][hapmap]
rs12098223	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12124059	0.92[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap];0.84[ASN][1000 genomes]
rs1616024	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs1633256	0.82[CHD][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs1633266	0.80[CEU][hapmap];0.93[EUR][1000 genomes]
rs1633267	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs16841642	0.90[CHD][hapmap]
rs1772407	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs1772408	0.86[GIH][hapmap]
rs1772414	0.93[CHD][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs1772415	0.90[CHD][hapmap];0.91[GIH][hapmap];0.84[TSI][hapmap]
rs1935067	0.90[CHD][hapmap]
rs2236584	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298803	0.87[CHD][hapmap]
rs2518555	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2518562	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs2570916	0.86[GIH][hapmap]
rs2793844	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2793845	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2814770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2814771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2852695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2852696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3018316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3737522	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3768514	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768515	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768519	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3768523	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6940	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs74122214	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74122232	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7532207	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs855865	0.95[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs856054	0.82[CEU][hapmap]
rs856055	0.94[GIH][hapmap];0.81[TSI][hapmap]
rs861318	0.91[GIH][hapmap];0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3754460	IFI16	cis	cerebellum	SCAN
rs3754460	AIM2	cis	lymphoblastoid	seeQTL
rs3754460	TMEM79	cis	parietal	SCAN
rs3754460	OR10R2	cis	parietal	SCAN
rs3754460	IFI16	cis	parietal	SCAN
rs3754460	AIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 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	chr1:158986000-159016200	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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