Variant report

Variant	rs41264457
Chromosome Location	chr1:159046378-159046379
allele	C/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	SIN3A	chr1:159046164-159047290	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:159046248-159047629	U87	brain:	n/a	n/a
3	POLR2A	chr1:159046218-159047553	GM15510	blood:	n/a	n/a
4	ELF1	chr1:159046275-159047457	GM12878	blood:	n/a	n/a
5	BCLAF1	chr1:159046183-159047596	GM12878	blood:	n/a	n/a
6	YY1	chr1:159046169-159046857	GM12878	blood:	n/a	chr1:159046294-159046310
7	POLR2A	chr1:159046222-159047580	GM18951	blood:	n/a	n/a
8	POLR2A	chr1:159046083-159047593	GM12892	blood:	n/a	n/a
9	MAX	chr1:159046130-159047502	GM12878	blood:	n/a	n/a
10	BHLHE40	chr1:159046263-159047436	K562	blood:	n/a	n/a
11	POLR2A	chr1:159046239-159047653	GM12891	blood:	n/a	n/a
12	TBL1XR1	chr1:159045989-159047797	GM12878	blood:	n/a	n/a
13	MTA3	chr1:159046256-159047630	GM12878	blood:	n/a	n/a
14	RELA	chr1:159046339-159047619	GM12878	blood:	n/a	n/a
15	STAT5A	chr1:159046322-159047605	GM12878	blood:	n/a	chr1:159046737-159046748
16	BATF	chr1:159046282-159047624	GM12878	blood:	n/a	n/a
17	RELA	chr1:159046178-159048034	GM18951	blood:	n/a	n/a
18	RELA	chr1:159046200-159047793	GM15510	blood:	n/a	n/a
19	WRNIP1	chr1:159046231-159047853	GM12878	blood:	n/a	n/a
20	POLR2A	chr1:159046073-159047557	GM12892	blood:	n/a	n/a
21	POLR2A	chr1:159046286-159047830	GM12878	blood:	n/a	n/a
22	POLR2A	chr1:159046146-159048461	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:159046181-159047554	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:159046043-159048043	GM12878	blood:	n/a	n/a
25	STAT1	chr1:159046363-159048018	Hela-S3	cervix:	n/a	chr1:159047092-159047103 chr1:159046737-159046748 chr1:159047113-159047124
26	TAF1	chr1:159046345-159046668	GM12878	blood:	n/a	n/a
27	EP300	chr1:159046345-159047792	GM12878	blood:	n/a	chr1:159046703-159046712
28	RELA	chr1:159046203-159048021	GM12891	blood:	n/a	n/a
29	POLR2A	chr1:159046123-159047613	GM12892	blood:	n/a	n/a
30	POU2F2	chr1:159046235-159046722	GM12891	blood:	n/a	n/a
31	POU2F2	chr1:159046347-159047243	GM12878	blood:	n/a	n/a
32	FOXM1	chr1:159046347-159047634	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:159046079-159047624	GM12892	blood:	n/a	n/a
34	YY1	chr1:159046251-159047571	GM12878	blood:	n/a	chr1:159046294-159046310
35	MAZ	chr1:159046067-159047593	GM12878	blood:	n/a	n/a
36	BHLHE40	chr1:159046197-159047803	GM12878	blood:	n/a	n/a
37	STAT1	chr1:159046189-159047520	GM12878	blood:	n/a	chr1:159047092-159047103 chr1:159046737-159046748 chr1:159047113-159047124
38	YY1	chr1:159046220-159047587	GM12878	blood:	n/a	chr1:159046294-159046310
39	NR2F2	chr1:159046329-159047669	K562	blood:	n/a	n/a
40	CHD1	chr1:159045777-159047568	GM12878	blood:	n/a	n/a
41	RUNX3	chr1:159046272-159047700	GM12878	blood:	n/a	n/a
42	RCOR1	chr1:159046078-159047566	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:159046177-159047555	GM12892	blood:	n/a	n/a
44	POU2F2	chr1:159046335-159046691	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:159045986-159047745	U87	brain:	n/a	n/a
46	POLR2A	chr1:159046040-159048183	GM12878	blood:	n/a	n/a
47	TBP	chr1:159046077-159047780	GM12878	blood:	n/a	n/a
48	CREB1	chr1:159046302-159047679	GM12878	blood:	n/a	n/a
49	RELA	chr1:159046182-159048121	GM10847	blood:	n/a	n/a
50	ZNF143	chr1:159046238-159047603	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:159042502..159045008-chr1:159045227..159046853,2	K562	blood:
2	chr1:158656464..158659384-chr1:159045094..159048407,3	K562	blood:
3	chr1:158978448..158981430-chr1:159044743..159047016,2	K562	blood:

Variant related genes	Relation type
AIM2	TF binding region
ENSG00000163554	Chromatin interaction
ENSG00000163568	Chromatin interaction
ENSG00000163565	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12124059	0.84[ASN][1000 genomes]
rs16841642	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16841682	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1935067	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2298803	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2518562	0.95[ASN][1000 genomes]
rs2793845	0.87[ASN][1000 genomes]
rs55719948	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55791394	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs855865	0.84[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41264457	AIM2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159038600-159056400	Weak transcription	Spleen	Spleen
2	chr1:159039000-159046600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:159044200-159047200	Active TSS	GM12878-XiMat	blood
4	chr1:159044600-159046600	Active TSS	Primary B cells from peripheral blood	blood
5	chr1:159044800-159047200	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr1:159044800-159048200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
7	chr1:159045200-159047400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:159045400-159047600	Active TSS	Primary hematopoietic stem cells	blood
9	chr1:159045600-159046600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
10	chr1:159045800-159046600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
11	chr1:159045800-159046600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:159045800-159046600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:159045800-159046600	Active TSS	Duodenum Mucosa	Duodenum
14	chr1:159045800-159046600	Active TSS	Rectal Mucosa Donor 31	rectum
15	chr1:159046000-159046400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr1:159046000-159046600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr1:159046000-159046600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr1:159046000-159046600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr1:159046000-159048000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr1:159046200-159046400	Flanking Active TSS	Primary B cells from cord blood	blood
21	chr1:159046200-159046400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:159046200-159046600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr1:159046200-159046600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:159046200-159046600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:159046200-159046600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
26	chr1:159046200-159046600	Flanking Active TSS	Esophagus	oesophagus
27	chr1:159046200-159046800	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr1:159046200-159047000	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr1:159046200-159047200	Enhancers	Placenta	Placenta
30	chr1:159046200-159047600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:159046200-159048000	Flanking Active TSS	K562	blood
32	chr1:159046200-159048000	Enhancers	NHDF-Ad	bronchial
33	chr1:159046200-159048200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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