Variant report

Variant	rs12094741
Chromosome Location	chr1:158998665-158998666
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	STAT3	chr1:158998595-158998699	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
IFI16	TF binding region

Extended variants
information (count: 81 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1057027	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1057028	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1101991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1101993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1101994	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1101995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1101996	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1101998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265131	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11265132	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11265133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12061402	0.92[ASN][1000 genomes]
rs12087333	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12090965	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12093523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12094545	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12094786	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12098223	0.88[GIH][hapmap]
rs12120311	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12124059	0.80[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs12139793	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12144575	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12239136	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12240111	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1417804	0.82[EUR][1000 genomes]
rs1614182	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs1633256	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1633262	0.84[EUR][1000 genomes]
rs1633265	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs1772405	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs1772407	0.85[GIH][hapmap]
rs1772408	0.82[CEU][hapmap];0.92[GIH][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs1772414	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1772415	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2106094	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2106095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2157694	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2157695	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2239890	0.99[ASN][1000 genomes]
rs2518553	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2570916	0.82[CEU][hapmap];0.92[GIH][hapmap];0.84[TSI][hapmap]
rs2814770	0.84[GIH][hapmap]
rs2814771	0.85[GIH][hapmap]
rs2840312	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3737522	0.88[GIH][hapmap]
rs3754460	0.88[GIH][hapmap]
rs3768513	0.88[GIH][hapmap]
rs4531291	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4575082	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55853408	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56235865	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56248786	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56348543	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56374780	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60958912	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66831955	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67772786	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67843408	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73021886	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs74122214	0.95[ASN][1000 genomes]
rs7525853	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7535630	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7535856	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];0.81[TSI][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7538035	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7540687	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7545770	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs855865	0.82[CEU][hapmap];0.88[GIH][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs856050	0.99[ASN][1000 genomes]
rs856051	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs856052	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]
rs856053	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]
rs856054	0.91[CEU][hapmap];0.89[CHB][hapmap]
rs856055	1.00[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs856056	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs856057	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs856058	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]
rs861318	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs866484	0.84[JPT][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12094741	IFI16	cis	cerebellum	SCAN
rs12094741	AIM2	Cis_1M	lymphoblastoid	RTeQTL
rs12094741	IFI16	cis	parietal	SCAN
rs12094741	FCRL4	cis	cerebellum	SCAN
rs12094741	TMEM79	cis	parietal	SCAN

Chromatin state (count:99 , 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	chr1:158987200-159000000	Weak transcription	Small Intestine	intestine
14	chr1:158987200-159000200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr1:158987200-159000400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:158987200-159001200	Strong transcription	Fetal Thymus	thymus
17	chr1:158987800-159000200	Weak transcription	Esophagus	oesophagus
18	chr1:158988000-159002200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:158988200-159000000	Weak transcription	HSMMtube	muscle
20	chr1:158988200-159000200	Weak transcription	Left Ventricle	heart
21	chr1:158988200-159016600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr1:158988400-159002400	Weak transcription	Fetal Brain Male	brain
23	chr1:158988600-159024000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr1:158988800-158999000	Genic enhancers	Dnd41	blood
25	chr1:158988800-159000800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:158989000-159002400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:158989000-159003000	Weak transcription	Colonic Mucosa	Colon
28	chr1:158989800-159004200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:158990200-158999800	Weak transcription	Brain Hippocampus Middle	brain
30	chr1:158990200-159000200	Weak transcription	Brain Anterior Caudate	brain
31	chr1:158991000-159000000	Weak transcription	Placenta	Placenta
32	chr1:158991600-159000200	Weak transcription	Liver	Liver
33	chr1:158991600-159000200	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr1:158991600-159000200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:158991600-159000400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr1:158992400-159000200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:158993000-159023200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr1:158993800-159000600	Weak transcription	HMEC	breast
39	chr1:158993800-159002000	Weak transcription	NH-A	brain
40	chr1:158994000-159000200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:158994000-159000800	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:158994200-158998800	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:158994200-158999000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:158994400-159000000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:158994400-159000000	Weak transcription	Adipose Nuclei	Adipose
46	chr1:158994400-159000200	Weak transcription	Spleen	Spleen
47	chr1:158994400-159000400	Weak transcription	Colon Smooth Muscle	Colon
48	chr1:158994400-159000400	Weak transcription	NHDF-Ad	bronchial
49	chr1:158994600-159000200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr1:158994600-159000200	Weak transcription	Hela-S3	cervix

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