Variant report

Variant	rs12728586
Chromosome Location	chr1:158983022-158983023
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	POLR2A	chr1:158982898-158984553	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:158982037-158984384	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:158982888-158984463	GM12878	blood:	n/a	n/a
4	ZNF384	chr1:158982445-158983119	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:158981852-158987235	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr1:158978464-158986840	GM12892	blood:	n/a	n/a
7	CHD1	chr1:158981505-158983902	GM12878	blood:	n/a	n/a
8	POLR2A	chr1:158981523-158987265	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:158978384-158985943	GM19193	blood:	n/a	n/a
10	POLR2A	chr1:158982200-158983713	GM12892	blood:	n/a	n/a
11	E2F6	chr1:158982216-158983037	H1-hESC	embryonic stem cell:	n/a	n/a
12	MXI1	chr1:158982167-158983566	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:158981580-158990399	GM12891	blood:	n/a	n/a
14	POLR2A	chr1:158981297-158987303	GM12878	blood:	n/a	n/a
15	POLR2A	chr1:158978350-158987224	GM18505	blood:	n/a	n/a
16	POLR2A	chr1:158978475-158987184	GM19099	blood:	n/a	n/a
17	POLR2A	chr1:158982072-158983653	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
IFI16	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11539423	0.88[AMR][1000 genomes]
rs12734915	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12738378	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12739704	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12755219	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12756557	0.85[AFR][1000 genomes]
rs1361564	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1361565	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16841500	0.88[AMR][1000 genomes]
rs1956	0.88[AMR][1000 genomes]
rs4262539	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66519738	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72704976	0.88[AMR][1000 genomes]
rs7526724	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs856047	0.85[AMR][1000 genomes]

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

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158976000-159000800	Weak transcription	Gastric	stomach
2	chr1:158977200-158990400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:158978600-158984200	Active TSS	Rectal Smooth Muscle	rectum
4	chr1:158978800-158983800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:158978800-158985800	Active TSS	Rectal Mucosa Donor 29	rectum
6	chr1:158979200-158983200	Active TSS	Rectal Mucosa Donor 31	rectum
7	chr1:158979200-158983400	Active TSS	Right Atrium	heart
8	chr1:158979200-158984000	Active TSS	Stomach Smooth Muscle	stomach
9	chr1:158979400-158983200	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr1:158979400-158983200	Active TSS	Skeletal Muscle Male	skeletal muscle
11	chr1:158979400-158983400	Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr1:158979400-158983600	Active TSS	Fetal Muscle Leg	muscle
13	chr1:158979400-158983600	Active TSS	Placenta	Placenta
14	chr1:158979400-158983800	Active TSS	Liver	Liver
15	chr1:158979400-158984000	Active TSS	Brain Hippocampus Middle	brain
16	chr1:158979400-158984000	Active TSS	GM12878-XiMat	blood
17	chr1:158979400-158984400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:158979400-158984400	Active TSS	Brain Anterior Caudate	brain
19	chr1:158979400-158984400	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr1:158979600-158983200	Active TSS	Primary B cells from peripheral blood	blood
21	chr1:158979600-158983400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:158979600-158983400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr1:158979600-158983400	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr1:158979800-158984600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:158980000-158983400	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr1:158980200-159025400	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:158981200-158983200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:158981200-158985400	Weak transcription	Fetal Intestine Small	intestine
29	chr1:158981200-158985400	Weak transcription	Pancreas	Pancrea
30	chr1:158981200-158986400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr1:158981600-158983800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:158981600-158983800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:158981600-158984200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:158981600-158986000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr1:158982000-158983800	Active TSS	Duodenum Mucosa	Duodenum
36	chr1:158982000-158984000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
37	chr1:158982000-158988000	Weak transcription	Fetal Brain Male	brain
38	chr1:158982200-158983200	Active TSS	Lung	lung
39	chr1:158982200-158983400	Active TSS	Psoas Muscle	Psoas
40	chr1:158982200-158983400	Active TSS	Sigmoid Colon	Sigmoid Colon
41	chr1:158982200-158983400	Flanking Active TSS	Dnd41	blood
42	chr1:158982200-158983600	Active TSS	Right Ventricle	heart
43	chr1:158982200-158984200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:158982400-158983200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
45	chr1:158982400-158983400	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr1:158982400-158983400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:158982400-158983600	Active TSS	Colonic Mucosa	Colon
48	chr1:158982600-158983200	Active TSS	Adipose Nuclei	Adipose
49	chr1:158982600-158983200	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr1:158982600-158983400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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