Variant report

Variant	rs3925162
Chromosome Location	chr19:45639716-45639717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:29)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:29 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:45639525-45641085	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:45639386-45641045	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:45639690-45641016	GM12892	blood:	n/a	n/a
4	POLR2A	chr19:45639677-45640203	GM12892	blood:	n/a	n/a
5	POLR2A	chr19:45639691-45640132	GM12878	blood:	n/a	n/a
6	POLR2A	chr19:45639326-45641397	GM12891	blood:	n/a	n/a
7	EBF1	chr19:45639525-45641042	GM12878	blood:	n/a	chr19:45640734-45640745
8	POLR2A	chr19:45639224-45641087	GM12878	blood:	n/a	n/a
9	MXI1	chr19:45639578-45640030	GM12878	blood:	n/a	n/a
10	POU2F2	chr19:45639631-45640260	GM12891	blood:	n/a	n/a
11	RUNX3	chr19:45639549-45640181	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:45639649-45641010	GM19193	blood:	n/a	n/a
13	SPI1	chr19:45639708-45640116	GM12878	blood:	n/a	n/a
14	ELF1	chr19:45639624-45640522	GM12878	blood:	n/a	n/a
15	SPI1	chr19:45639656-45640141	GM12891	blood:	n/a	n/a
16	POLR2A	chr19:45639639-45640150	GM12891	blood:	n/a	n/a
17	POLR2A	chr19:45639473-45641086	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:45639598-45640940	GM12878	blood:	n/a	n/a
19	RCOR1	chr19:45639520-45639983	GM12878	blood:	n/a	n/a
20	EP300	chr19:45639675-45640111	GM12878	blood:	n/a	n/a
21	USF2	chr19:45639688-45641111	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:45639609-45640181	GM12891	blood:	n/a	n/a
23	POLR2A	chr19:45639662-45640999	GM18951	blood:	n/a	n/a
24	POLR2A	chr19:45639576-45641018	GM12891	blood:	n/a	n/a
25	POLR2A	chr19:45639645-45641033	GM12892	blood:	n/a	n/a
26	POLR2A	chr19:45639604-45640260	GM12891	blood:	n/a	n/a
27	MTA3	chr19:45639324-45641142	GM12878	blood:	n/a	n/a
28	SPI1	chr19:45639712-45640099	GM12891	blood:	n/a	n/a
29	SPI1	chr19:45639460-45641085	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45580675..45582484-chr19:45637452..45640125,3	MCF-7	breast:
2	chr19:45637342..45640694-chr19:45642011..45644916,3	K562	blood:
3	chr19:45639467..45643704-chr19:45647170..45652290,6	K562	blood:
4	chr19:45639686..45641880-chr19:45681901..45684356,2	MCF-7	breast:
5	chr19:45638752..45643704-chr19:45645351..45650444,8	K562	blood:
6	chr19:45628639..45633572-chr19:45633990..45640719,7	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NKPD1-1	chr19:45639307-45641075	ENSG00000250044

No data

Variant related genes	Relation type
PPP1R37	TF binding region
ENSG00000267346	Chromatin interaction
ENSG00000189114	Chromatin interaction
ENSG00000142252	Chromatin interaction
ENSG00000267545	Chromatin interaction
ENSG00000104866	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1005451	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10401157	0.97[ASN][1000 genomes]
rs10401823	0.94[ASN][1000 genomes]
rs10408847	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs10413253	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10416500	0.87[ASN][1000 genomes]
rs10420562	0.92[ASN][1000 genomes]
rs10425074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048699	0.97[ASN][1000 genomes]
rs1114831	0.97[ASN][1000 genomes]
rs1114832	0.97[ASN][1000 genomes]
rs12459074	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12462040	0.97[ASN][1000 genomes]
rs2004357	0.97[ASN][1000 genomes]
rs2041262	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28469095	0.92[ASN][1000 genomes]
rs28620490	0.97[ASN][1000 genomes]
rs34545713	0.97[ASN][1000 genomes]
rs57565080	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7248421	0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912142	chr19:45570051-45708758	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833842	chr19:45593888-45684308	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv833843	chr19:45593888-45793682	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv912143	chr19:45624303-45767214	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv3403042	chr19:45626786-45874859	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv912144	chr19:45636319-45687446	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45610400-45644400	Weak transcription	Aorta	Aorta
2	chr19:45617000-45651600	Weak transcription	Fetal Kidney	kidney
3	chr19:45617800-45640000	Weak transcription	Fetal Lung	lung
4	chr19:45620800-45643800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr19:45621200-45639800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr19:45621200-45644000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr19:45621600-45643800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:45621800-45639800	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:45625000-45654200	Weak transcription	NHDF-Ad	bronchial
10	chr19:45626200-45644400	Weak transcription	Ovary	ovary
11	chr19:45626200-45653400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:45627200-45640000	Weak transcription	Adipose Nuclei	Adipose
13	chr19:45627600-45655600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:45627800-45644000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr19:45629400-45639800	Weak transcription	Right Ventricle	heart
16	chr19:45629400-45644000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr19:45629600-45640000	Weak transcription	Placenta	Placenta
18	chr19:45629600-45640000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr19:45629600-45643800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr19:45629600-45644600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr19:45629800-45639800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr19:45629800-45639800	Weak transcription	Right Atrium	heart
23	chr19:45629800-45643800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:45629800-45643800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:45629800-45644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr19:45630000-45639800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr19:45630000-45641400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr19:45630800-45653200	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr19:45631800-45641400	Strong transcription	Fetal Stomach	stomach
30	chr19:45632600-45643000	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:45632600-45643400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr19:45632600-45643600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:45633600-45643000	Weak transcription	Lung	lung
34	chr19:45633600-45655200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr19:45633800-45642800	Weak transcription	Dnd41	blood
36	chr19:45634200-45639800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:45634200-45639800	Weak transcription	Gastric	stomach
38	chr19:45634200-45639800	Weak transcription	HSMMtube	muscle
39	chr19:45634200-45641400	Strong transcription	Fetal Intestine Small	intestine
40	chr19:45634200-45644400	Weak transcription	NHEK	skin
41	chr19:45634200-45645000	Weak transcription	HUVEC	blood vessel
42	chr19:45634400-45639800	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr19:45634400-45640000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr19:45634400-45641200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr19:45634400-45641600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr19:45634400-45653000	Weak transcription	NH-A	brain
47	chr19:45634600-45641400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:45634600-45641400	Weak transcription	Esophagus	oesophagus
49	chr19:45636600-45641800	Enhancers	Primary B cells from peripheral blood	blood
50	chr19:45637000-45641600	Enhancers	Primary B cells from cord blood	blood

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