Variant report

Variant	rs12124059
Chromosome Location	chr1:159026639-159026640
allele	C/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	chr1:159023373-159027389	GM18505	blood:	n/a	n/a
2	POLR2A	chr1:159025628-159027421	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:159025499-159028253	U87	brain:	n/a	n/a
4	POLR2A	chr1:159025559-159027249	GM12892	blood:	n/a	n/a
5	POLR2A	chr1:159023796-159027402	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:159024964-159027320	GM18951	blood:	n/a	n/a
7	POLR2A	chr1:159026549-159026971	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr1:159025611-159027290	GM12891	blood:	n/a	n/a
9	POLR2A	chr1:159026521-159027346	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:159019870-159029996	GM12878	blood:	n/a	n/a
11	MTA3	chr1:159025619-159027431	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:159026547-159026726	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:159020046-159029918	GM12891	blood:	n/a	n/a
14	POLR2A	chr1:159025587-159027219	GM12892	blood:	n/a	n/a
15	POLR2A	chr1:159025603-159026880	GM12892	blood:	n/a	n/a
16	POLR2A	chr1:159026309-159028253	U87	brain:	n/a	n/a
17	POLR2A	chr1:159025804-159027040	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000265589	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1057027	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs1057028	1.00[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs1101991	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs1101993	0.80[CEU][hapmap]
rs1101998	0.80[CEU][hapmap];0.88[GIH][hapmap]
rs11265132	0.83[EUR][1000 genomes]
rs11265133	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs11265134	0.83[ASN][1000 genomes]
rs12090965	0.83[EUR][1000 genomes]
rs12093523	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs12094545	0.83[EUR][1000 genomes]
rs12094692	0.83[EUR][1000 genomes]
rs12094741	0.80[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs12094786	0.83[EUR][1000 genomes]
rs12098223	0.92[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs12144575	0.83[EUR][1000 genomes]
rs12239136	0.83[EUR][1000 genomes]
rs12240111	0.83[EUR][1000 genomes]
rs1417804	0.87[EUR][1000 genomes]
rs1614182	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1633256	1.00[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs1633262	0.88[EUR][1000 genomes]
rs1633265	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs16841642	0.89[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs1772405	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1772407	0.82[GIH][hapmap];0.80[TSI][hapmap]
rs1772408	1.00[CEU][hapmap];0.88[GIH][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs1772414	1.00[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1772415	1.00[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes]
rs1935067	0.89[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2106094	0.83[EUR][1000 genomes]
rs2106095	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs2157694	0.83[EUR][1000 genomes]
rs2157695	0.83[EUR][1000 genomes]
rs2236584	0.87[ASN][1000 genomes]
rs2298803	0.88[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs2518553	0.90[EUR][1000 genomes]
rs2518555	0.87[ASN][1000 genomes]
rs2518562	0.94[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap]
rs2570916	1.00[CEU][hapmap];0.88[GIH][hapmap];0.97[TSI][hapmap]
rs2793844	0.87[ASN][1000 genomes]
rs2793845	0.97[ASN][1000 genomes]
rs2814770	0.86[CHD][hapmap];0.81[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2814771	0.92[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];0.80[TSI][hapmap];0.85[ASN][1000 genomes]
rs2840312	0.83[EUR][1000 genomes]
rs2852695	0.80[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2852696	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2994824	1.00[YRI][hapmap]
rs3018316	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs3737522	0.92[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs3754460	0.92[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.80[TSI][hapmap];0.84[ASN][1000 genomes]
rs3768513	0.92[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs3768514	0.84[ASN][1000 genomes]
rs3768515	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs3768519	0.84[ASN][1000 genomes]
rs3768523	0.83[ASN][1000 genomes]
rs41264457	0.84[ASN][1000 genomes]
rs55719948	0.83[ASN][1000 genomes]
rs55791394	0.83[ASN][1000 genomes]
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]
rs6940	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs73021886	0.83[EUR][1000 genomes]
rs74122232	0.84[ASN][1000 genomes]
rs7532207	0.87[ASN][1000 genomes]
rs7535630	0.83[EUR][1000 genomes]
rs7535856	0.82[GIH][hapmap]
rs7538035	0.83[EUR][1000 genomes]
rs7545770	0.83[EUR][1000 genomes]
rs855865	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs855866	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs856051	0.83[EUR][1000 genomes]
rs856052	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs856053	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs856054	0.90[CEU][hapmap]
rs856055	0.93[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs856056	0.90[EUR][1000 genomes]
rs856057	0.90[EUR][1000 genomes]
rs856058	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs861318	1.00[CEU][hapmap];0.88[GIH][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]

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
rs12124059	TMEM79	cis	parietal	SCAN
rs12124059	IFI16	cis	cerebellum	SCAN
rs12124059	AIM2	cis	lymphoblastoid	seeQTL
rs12124059	AIM2	Cis_1M	lymphoblastoid	RTeQTL
rs12124059	FCRL4	cis	cerebellum	SCAN
rs12124059	IFI16	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158982600-159027400	Weak transcription	Fetal Kidney	kidney
2	chr1:158984800-159027400	Weak transcription	Psoas Muscle	Psoas
3	chr1:158998800-159033800	Weak transcription	Fetal Brain Female	brain
4	chr1:159001000-159027400	Weak transcription	Right Ventricle	heart
5	chr1:159001400-159036200	Weak transcription	Small Intestine	intestine
6	chr1:159001600-159028400	Strong transcription	Fetal Thymus	thymus
7	chr1:159005600-159027200	Weak transcription	Brain Angular Gyrus	brain
8	chr1:159007200-159026800	Weak transcription	Pancreas	Pancrea
9	chr1:159009200-159030400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:159017000-159026800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr1:159020200-159026800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:159020200-159027000	Strong transcription	Thymus	Thymus
13	chr1:159020200-159027200	Strong transcription	GM12878-XiMat	blood
14	chr1:159021200-159028400	Weak transcription	Fetal Intestine Small	intestine
15	chr1:159021400-159027000	Strong transcription	Rectal Smooth Muscle	rectum
16	chr1:159021800-159028000	Weak transcription	Gastric	stomach
17	chr1:159022400-159028800	Weak transcription	Brain Substantia Nigra	brain
18	chr1:159022600-159031600	Weak transcription	Fetal Brain Male	brain
19	chr1:159022800-159029600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
20	chr1:159022800-159037400	Genic enhancers	Primary B cells from peripheral blood	blood
21	chr1:159023000-159027000	Genic enhancers	Primary B cells from cord blood	blood
22	chr1:159023800-159027000	Genic enhancers	Spleen	Spleen
23	chr1:159024000-159027600	Genic enhancers	Primary monocytes fromperipheralblood	blood
24	chr1:159024200-159026800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr1:159024200-159028600	Weak transcription	Brain Anterior Caudate	brain
26	chr1:159024200-159032400	Weak transcription	Brain Germinal Matrix	brain
27	chr1:159024400-159027800	Weak transcription	Aorta	Aorta
28	chr1:159024400-159028800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:159024400-159030800	Weak transcription	Placenta	Placenta
30	chr1:159024600-159027000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:159024800-159027200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr1:159024800-159027200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:159025200-159026800	Weak transcription	Liver	Liver
34	chr1:159025200-159037600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr1:159025200-159038200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:159025400-159027000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr1:159025400-159027000	Weak transcription	NH-A	brain
38	chr1:159025400-159027400	Strong transcription	Primary T cells from cord blood	blood
39	chr1:159025400-159027600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:159025400-159027800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr1:159025400-159029400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr1:159025400-159037400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
43	chr1:159025400-159037800	Weak transcription	NHDF-Ad	bronchial
44	chr1:159025400-159038200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr1:159025600-159027000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr1:159025600-159027000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:159025600-159027000	Strong transcription	Fetal Stomach	stomach
48	chr1:159025600-159036400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:159025800-159027200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr1:159025800-159029200	Weak transcription	HSMM	muscle

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