Variant report

Variant	rs12459567
Chromosome Location	chr19:40789926-40789927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:51)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:51 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:40789333-40791875	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:40788968-40790490	HepG2	liver:	n/a	n/a
3	FOXA1	chr19:40789319-40790054	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:40789296-40790059	HepG2	liver:	n/a	n/a
5	MAX	chr19:40789666-40790023	K562	blood:	n/a	n/a
6	POLR2A	chr19:40788195-40792187	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr19:40789385-40791876	GM12878	blood:	n/a	n/a
8	POLR2A	chr19:40788136-40791242	GM12878	blood:	n/a	n/a
9	CHD2	chr19:40789629-40789952	HepG2	liver:	n/a	n/a
10	MXI1	chr19:40789687-40792059	IMR90	lung:	n/a	n/a
11	FOXA2	chr19:40789593-40789928	HepG2	liver:	n/a	n/a
12	POLR2A	chr19:40789056-40790872	GM12892	blood:	n/a	n/a
13	MAZ	chr19:40789291-40789949	HepG2	liver:	n/a	n/a
14	FOXA1	chr19:40789397-40789974	HepG2	liver:	n/a	n/a
15	POLR2A	chr19:40789377-40789961	HepG2	liver:	n/a	n/a
16	ZNF263	chr19:40789127-40790796	HEK293-T-REx	kidney:	n/a	chr19:40789676-40789685
17	MXI1	chr19:40789629-40791833	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:40789062-40789989	GM12891	blood:	n/a	n/a
19	UBTF	chr19:40789601-40790066	K562	blood:	n/a	n/a
20	CHD1	chr19:40789834-40791914	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:40788900-40790001	K562	blood:	n/a	n/a
22	HEY1	chr19:40789285-40789928	K562	blood:	n/a	n/a
23	POLR2A	chr19:40789317-40790015	GM12891	blood:	n/a	n/a
24	POLR2A	chr19:40789282-40789983	GM12878	blood:	n/a	n/a
25	POLR2A	chr19:40781762-40793937	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr19:40789144-40792048	GM12892	blood:	n/a	n/a
27	POLR2A	chr19:40787276-40792053	GM12878	blood:	n/a	n/a
28	WRNIP1	chr19:40789765-40790706	GM12878	blood:	n/a	n/a
29	POLR2A	chr19:40789235-40791994	GM12892	blood:	n/a	n/a
30	STAT5A	chr19:40789777-40790893	GM12878	blood:	n/a	chr19:40790261-40790269 chr19:40790836-40790848 chr19:40790453-40790464
31	POLR2A	chr19:40789313-40790066	HepG2	liver:	n/a	n/a
32	MTA3	chr19:40789622-40791270	GM12878	blood:	n/a	n/a
33	POLR2A	chr19:40789156-40790050	K562	blood:	n/a	n/a
34	CHD1	chr19:40789452-40792116	IMR90	lung:	n/a	n/a
35	POLR2A	chr19:40789238-40789975	HepG2	liver:	n/a	n/a
36	POLR2A	chr19:40789051-40791950	K562	blood:	n/a	n/a
37	SIN3AK20	chr19:40787407-40793117	PANC-1	pancreas:	n/a	n/a
38	TCF12	chr19:40789843-40792193	A549	lung:	n/a	n/a
39	SREBP1	chr19:40789027-40792196	GM12878	blood:	n/a	n/a
40	EP300	chr19:40789395-40789934	HepG2	liver:	n/a	chr19:40789594-40789610
41	HEY1	chr19:40789421-40790039	HepG2	liver:	n/a	n/a
42	POLR2A	chr19:40789272-40791877	GM19193	blood:	n/a	n/a
43	POLR2A	chr19:40789242-40791248	GM12891	blood:	n/a	n/a
44	FOXA1	chr19:40789642-40789958	HepG2	liver:	n/a	n/a
45	FOXA1	chr19:40789512-40790034	HepG2	liver:	n/a	n/a
46	RCOR1	chr19:40789224-40789954	HepG2	liver:	n/a	n/a
47	MXI1	chr19:40789278-40789995	HepG2	liver:	n/a	n/a
48	POLR2A	chr19:40788818-40791904	HepG2	liver:	n/a	n/a
49	POLR2A	chr19:40789331-40791959	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:40789354-40791990	GM12891	blood:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40695407..40698481-chr19:40788292..40792778,5	K562	blood:
2	chr19:40789879..40793059-chr19:40870323..40872928,3	K562	blood:
3	chr19:40788680..40791212-chr19:40852795..40854366,2	K562	blood:

No data

Variant related genes	Relation type
AKT2	TF binding region
MIR641	TF binding region
ENSG00000160392	Chromatin interaction
ENSG00000130758	Chromatin interaction
ENSG00000105223	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12151335	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12460555	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12460615	0.80[ASN][1000 genomes]
rs12977474	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12985477	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962639	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1991460	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304186	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2368575	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs33933140	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35562135	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3745195	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4479364	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4502340	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4524046	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4802072	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803324	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803325	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4803326	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4803327	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55710016	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57158010	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58502633	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59263025	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7259273	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7507651	0.81[EUR][1000 genomes]
rs7508513	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8110323	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs890773	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	esv1005660	chr19:40784738-40790835	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
7	esv3373348	chr19:40789637-40792485	Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40770200-40790200	Weak transcription	Aorta	Aorta
2	chr19:40783400-40790000	Enhancers	Right Atrium	heart
3	chr19:40783800-40790600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:40786000-40790000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:40786400-40790200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:40787000-40790000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:40787000-40790000	Genic enhancers	Spleen	Spleen
8	chr19:40787200-40790000	Weak transcription	Small Intestine	intestine
9	chr19:40787800-40790400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr19:40788400-40790000	Enhancers	Gastric	stomach
11	chr19:40788400-40790200	Enhancers	Esophagus	oesophagus
12	chr19:40788600-40790200	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr19:40788800-40790000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:40788800-40790200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:40788800-40790400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr19:40788800-40790600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:40789000-40790000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:40789000-40790000	Transcr. at gene 5' and 3'	K562	blood
19	chr19:40789000-40790200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr19:40789000-40790600	Flanking Active TSS	Liver	Liver
21	chr19:40789000-40790600	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr19:40789200-40790000	Enhancers	Ovary	ovary
23	chr19:40789200-40790200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:40789200-40790200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr19:40789200-40790200	Flanking Active TSS	GM12878-XiMat	blood
26	chr19:40789200-40790400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr19:40789200-40790400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr19:40789200-40790400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr19:40789200-40790400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:40789200-40790400	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr19:40789200-40790400	Flanking Active TSS	Brain Hippocampus Middle	brain
32	chr19:40789200-40790400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
33	chr19:40789200-40790400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr19:40789200-40790400	Flanking Active TSS	HSMM	muscle
35	chr19:40789200-40790400	Flanking Active TSS	NHDF-Ad	bronchial
36	chr19:40789200-40790600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr19:40789200-40790600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:40789200-40790600	Flanking Active TSS	Osteobl	bone
39	chr19:40789200-40790800	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr19:40789400-40790000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:40789400-40790000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr19:40789400-40790000	Flanking Active TSS	HSMMtube	muscle
43	chr19:40789400-40790200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:40789400-40790200	Enhancers	Placenta	Placenta
45	chr19:40789400-40790200	Flanking Active TSS	Psoas Muscle	Psoas
46	chr19:40789400-40790200	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr19:40789400-40790400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:40789400-40790400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:40789400-40790400	Flanking Active TSS	Brain Angular Gyrus	brain
50	chr19:40789400-40790400	Flanking Active TSS	Brain Anterior Caudate	brain

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