Variant report

Variant	rs28537976
Chromosome Location	chr19:42780376-42780377
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	chr19:42780088-42781131	GM12891	blood:	n/a	n/a
2	POLR2A	chr19:42779871-42780671	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr19:42780160-42780663	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:42779995-42781263	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:42744297..42761073-chr19:42776978..42802286,113	MCF-7	breast:
2	chr19:42743599..42762610-chr19:42780302..42801550,102	MCF-7	breast:

Variant related genes	Relation type
CIC	TF binding region
ENSG00000105723	Chromatin interaction
ENSG00000105722	Chromatin interaction
ENSG00000268643	Chromatin interaction
ENSG00000204957	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10410185	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410198	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10410698	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412833	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10426306	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10426310	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11557114	0.91[ASN][1000 genomes]
rs11878620	0.91[ASN][1000 genomes]
rs11882654	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1206009	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1206027	0.84[EUR][1000 genomes]
rs1206031	0.80[EUR][1000 genomes]
rs1206035	0.84[EUR][1000 genomes]
rs1206038	0.84[EUR][1000 genomes]
rs1206040	0.84[EUR][1000 genomes]
rs1206041	0.84[EUR][1000 genomes]
rs1206042	0.84[EUR][1000 genomes]
rs1206044	0.84[EUR][1000 genomes]
rs1209280	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1211265	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13346991	0.84[EUR][1000 genomes]
rs1613100	0.82[EUR][1000 genomes]
rs1654623	0.82[EUR][1000 genomes]
rs1676211	0.84[EUR][1000 genomes]
rs1676213	0.82[EUR][1000 genomes]
rs1676215	0.82[EUR][1000 genomes]
rs1676217	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1676220	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1676221	0.84[EUR][1000 genomes]
rs2267630	0.87[ASN][1000 genomes]
rs2302485	0.91[ASN][1000 genomes]
rs2537697	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2615614	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28621009	0.80[EUR][1000 genomes]
rs35493131	0.91[ASN][1000 genomes]
rs35557987	0.80[EUR][1000 genomes]
rs3810148	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4141062	0.95[ASN][1000 genomes]
rs57938324	1.00[ASN][1000 genomes]
rs7255956	0.84[EUR][1000 genomes]
rs7258795	1.00[ASN][1000 genomes]
rs7260287	0.84[EUR][1000 genomes]
rs73552881	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73552895	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs741070	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs851296	0.82[EUR][1000 genomes]
rs851612	0.95[ASN][1000 genomes]
rs851615	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs862228	0.84[EUR][1000 genomes]
rs865436	0.84[EUR][1000 genomes]
rs9636121	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	esv1794508	chr19:42580026-42791462	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
7	nsv833833	chr19:42657276-42783122	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS 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	62 gene(s)	inside rSNPs	diseases
9	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
10	nsv833834	chr19:42736444-42835027	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	42 gene(s)	inside rSNPs	diseases
11	nsv911784	chr19:42741124-42787664	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	36 gene(s)	inside rSNPs	diseases
12	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
13	nsv911786	chr19:42744234-42797959	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	39 gene(s)	inside rSNPs	diseases
14	esv1802977	chr19:42754437-42789945	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
15	esv1801251	chr19:42768288-42788467	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
16	esv1803455	chr19:42768288-42788467	Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
17	esv1803706	chr19:42768288-42788467	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
18	esv1801291	chr19:42772432-42788467	Flanking Active TSS Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
19	esv1801294	chr19:42772432-42788467	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak 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	21 gene(s)	inside rSNPs	diseases
20	esv1801914	chr19:42772432-42788467	Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	21 gene(s)	inside rSNPs	diseases
21	nsv911787	chr19:42773862-42795554	Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak 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	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42774400-42783600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr19:42775400-42781400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr19:42775400-42781800	Weak transcription	Small Intestine	intestine
4	chr19:42775400-42782000	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr19:42775600-42781400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr19:42775800-42780400	Strong transcription	Fetal Stomach	stomach
7	chr19:42775800-42780600	Weak transcription	Fetal Heart	heart
8	chr19:42775800-42780600	Genic enhancers	Spleen	Spleen
9	chr19:42775800-42781600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr19:42775800-42781800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr19:42775800-42782400	Weak transcription	Fetal Kidney	kidney
12	chr19:42775800-42783600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:42776000-42780800	Genic enhancers	Esophagus	oesophagus
14	chr19:42776000-42780800	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr19:42776000-42781200	Weak transcription	Stomach Mucosa	stomach
16	chr19:42776000-42781600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr19:42776200-42780800	Strong transcription	Aorta	Aorta
18	chr19:42776200-42781800	Strong transcription	Fetal Thymus	thymus
19	chr19:42776400-42780800	Strong transcription	Fetal Intestine Small	intestine
20	chr19:42776400-42781400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
21	chr19:42776400-42782200	Genic enhancers	Pancreas	Pancrea
22	chr19:42777000-42782200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr19:42777200-42781400	Strong transcription	HepG2	liver
24	chr19:42777400-42781400	Strong transcription	Fetal Lung	lung
25	chr19:42777600-42781200	Genic enhancers	Liver	Liver
26	chr19:42777800-42780800	Genic enhancers	Brain Germinal Matrix	brain
27	chr19:42777800-42781000	Genic enhancers	Stomach Smooth Muscle	stomach
28	chr19:42777800-42782000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:42778000-42780600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:42778000-42781800	Genic enhancers	Fetal Muscle Leg	muscle
31	chr19:42778000-42783200	Genic enhancers	Placenta	Placenta
32	chr19:42778200-42780400	Genic enhancers	HMEC	breast
33	chr19:42778200-42780600	Genic enhancers	Lung	lung
34	chr19:42778200-42781000	Genic enhancers	Gastric	stomach
35	chr19:42778200-42781400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
36	chr19:42778200-42783400	Genic enhancers	Fetal Muscle Trunk	muscle
37	chr19:42778400-42783400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr19:42778400-42783800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:42778600-42780600	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr19:42778600-42781000	Genic enhancers	HSMMtube	muscle
41	chr19:42778600-42781800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr19:42778600-42782000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr19:42778800-42780600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:42778800-42780600	Genic enhancers	HSMM	muscle
45	chr19:42778800-42780800	Strong transcription	Primary B cells from cord blood	blood
46	chr19:42778800-42780800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr19:42778800-42780800	Genic enhancers	Brain Cingulate Gyrus	brain
48	chr19:42778800-42781800	Genic enhancers	Muscle Satellite Cultured Cells	--
49	chr19:42778800-42781800	Genic enhancers	NHEK	skin
50	chr19:42778800-42782400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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