Variant report

Variant	rs12727764
Chromosome Location	chr1:158982477-158982478
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:67)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:67 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAF1	chr1:158982258-158982683	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:158982079-158982782	U87	brain:	n/a	n/a
3	E2F4	chr1:158981857-158982942	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr1:158982216-158982807	MCF10A-Er-Src	breast:	n/a	chr1:158982400-158982411
5	POLR2A	chr1:158982223-158982753	PFSK-1	brain:	n/a	n/a
6	POLR2A	chr1:158982007-158982916	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr1:158982037-158984384	GM12892	blood:	n/a	n/a
8	SIN3A	chr1:158982241-158982702	GM12878	blood:	n/a	n/a
9	TAF1	chr1:158982231-158982573	PFSK-1	brain:	n/a	n/a
10	NFYB	chr1:158982272-158982643	GM12878	blood:	n/a	n/a
11	POLR2A	chr1:158981850-158982712	PFSK-1	brain:	n/a	n/a
12	ZNF143	chr1:158982348-158982632	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:158982261-158982606	GM12878	blood:	n/a	n/a
14	NFIC	chr1:158982106-158982880	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:158982021-158982850	GM12892	blood:	n/a	n/a
16	MTA3	chr1:158982184-158982701	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:158982300-158982639	GM12878	blood:	n/a	n/a
18	E2F6	chr1:158982317-158982720	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:158982130-158982786	GM12892	blood:	n/a	n/a
20	ZNF384	chr1:158982445-158983119	GM12878	blood:	n/a	n/a
21	MAX	chr1:158982276-158982734	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr1:158981971-158982862	U87	brain:	n/a	n/a
23	POLR2A	chr1:158981852-158987235	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr1:158978464-158986840	GM12892	blood:	n/a	n/a
25	MAX	chr1:158982195-158982832	GM12878	blood:	n/a	n/a
26	STAT3	chr1:158982112-158982701	MCF10A-Er-Src	breast:	n/a	chr1:158982400-158982411
27	PBX3	chr1:158982325-158982512	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:158982219-158982658	Raji	blood:	n/a	n/a
29	POLR2A	chr1:158982081-158982759	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:158982185-158982691	GM12891	blood:	n/a	n/a
31	MAX	chr1:158982391-158982671	H1-hESC	embryonic stem cell:	n/a	n/a
32	WRNIP1	chr1:158982265-158982635	GM12878	blood:	n/a	n/a
33	CHD1	chr1:158981505-158983902	GM12878	blood:	n/a	n/a
34	PML	chr1:158982015-158982795	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:158981523-158987265	GM12878	blood:	n/a	n/a
36	PML	chr1:158982271-158982563	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:158978384-158985943	GM19193	blood:	n/a	n/a
38	POLR2A	chr1:158982019-158982905	U87	brain:	n/a	n/a
39	CREB1	chr1:158982199-158982795	GM12878	blood:	n/a	n/a
40	MAX	chr1:158982331-158982679	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr1:158982200-158983713	GM12892	blood:	n/a	n/a
42	MAX	chr1:158982342-158982636	H1-hESC	embryonic stem cell:	n/a	n/a
43	FOS	chr1:158982027-158982675	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr1:158982202-158982647	GM12891	blood:	n/a	n/a
45	REST	chr1:158982351-158982644	PFSK-1	brain:	n/a	n/a
46	E2F6	chr1:158982216-158983037	H1-hESC	embryonic stem cell:	n/a	n/a
47	MYC	chr1:158981840-158982656	MCF10A-Er-Src	breast:	n/a	n/a
48	POLR2A	chr1:158982147-158982801	HUVEC	blood vessel:	n/a	n/a
49	POLR2A	chr1:158982147-158982740	GM12891	blood:	n/a	n/a
50	MXI1	chr1:158982167-158983566	GM12878	blood:	n/a	n/a

No data

Variant related genes	Relation type
IFI16	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1101998	0.85[MEX][hapmap]
rs12738378	0.91[MEX][hapmap]
rs12756557	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1361564	0.92[MEX][hapmap]
rs1361565	0.92[MEX][hapmap]
rs7535856	0.85[MEX][hapmap]
rs856064	0.86[TSI][hapmap]
rs866484	0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3376764	chr1:158761947-158998617	Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	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
3	nsv3176	chr1:158955373-158986568	Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	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
rs12727764	ADAR	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158976000-158983000	Weak transcription	Spleen	Spleen
2	chr1:158976000-159000800	Weak transcription	Gastric	stomach
3	chr1:158977200-158990400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr1:158978600-158984200	Active TSS	Rectal Smooth Muscle	rectum
5	chr1:158978800-158983800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:158978800-158985800	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr1:158979200-158982600	Active TSS	Fetal Stomach	stomach
8	chr1:158979200-158982800	Active TSS	NHLF	lung
9	chr1:158979200-158983200	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr1:158979200-158983400	Active TSS	Right Atrium	heart
11	chr1:158979200-158984000	Active TSS	Stomach Smooth Muscle	stomach
12	chr1:158979400-158982800	Active TSS	Fetal Intestine Large	intestine
13	chr1:158979400-158983000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:158979400-158983000	Active TSS	Primary T cells fromperipheralblood	blood
15	chr1:158979400-158983000	Active TSS	Ovary	ovary
16	chr1:158979400-158983000	Active TSS	Thymus	Thymus
17	chr1:158979400-158983200	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr1:158979400-158983200	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr1:158979400-158983400	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr1:158979400-158983600	Active TSS	Fetal Muscle Leg	muscle
21	chr1:158979400-158983600	Active TSS	Placenta	Placenta
22	chr1:158979400-158983800	Active TSS	Liver	Liver
23	chr1:158979400-158984000	Active TSS	Brain Hippocampus Middle	brain
24	chr1:158979400-158984000	Active TSS	GM12878-XiMat	blood
25	chr1:158979400-158984400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr1:158979400-158984400	Active TSS	Brain Anterior Caudate	brain
27	chr1:158979400-158984400	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr1:158979600-158982800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:158979600-158983000	Active TSS	Primary monocytes fromperipheralblood	blood
30	chr1:158979600-158983000	Active TSS	Fetal Thymus	thymus
31	chr1:158979600-158983200	Active TSS	Primary B cells from peripheral blood	blood
32	chr1:158979600-158983400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:158979600-158983400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr1:158979600-158983400	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr1:158979800-158984600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:158980000-158983400	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:158980400-158983000	Active TSS	Primary T cells from cord blood	blood
39	chr1:158981000-158982800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr1:158981200-158982800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:158981200-158982800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:158981200-158983200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:158981200-158985400	Weak transcription	Fetal Intestine Small	intestine
44	chr1:158981200-158985400	Weak transcription	Pancreas	Pancrea
45	chr1:158981200-158986400	Weak transcription	Fetal Muscle Trunk	muscle
46	chr1:158981400-158982800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:158981600-158982600	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr1:158981600-158982800	Flanking Active TSS	Primary hematopoietic stem cells	blood
49	chr1:158981600-158982800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr1:158981600-158983000	Flanking Active TSS	HUVEC	blood vessel

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