Variant report

Variant	rs10408141
Chromosome Location	chr19:42780917-42780918
allele	C/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	chr19:42780809-42780957	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr19:42780088-42781131	GM12891	blood:	n/a	n/a
3	MTA3	chr19:42780769-42781430	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:42780645-42781230	K562	blood:	n/a	n/a
5	POLR2A	chr19:42780799-42781500	PFSK-1	brain:	n/a	n/a
6	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
ENSG00000105722	Chromatin interaction
ENSG00000204957	Chromatin interaction
ENSG00000105723	Chromatin interaction
ENSG00000268643	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10403246	1.00[AMR][1000 genomes]
rs10406755	1.00[AMR][1000 genomes]
rs10410653	0.89[AFR][1000 genomes]
rs10411908	0.82[AFR][1000 genomes]
rs10412954	1.00[AMR][1000 genomes]
rs10413484	0.89[AFR][1000 genomes]
rs10414056	1.00[AMR][1000 genomes]
rs10415478	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10416241	1.00[AMR][1000 genomes]
rs10418493	1.00[AMR][1000 genomes]
rs10419013	1.00[AMR][1000 genomes]
rs10421026	1.00[AMR][1000 genomes]
rs10425883	1.00[AMR][1000 genomes]
rs13345986	1.00[AMR][1000 genomes]
rs28463673	0.82[AFR][1000 genomes]
rs28469564	0.89[AFR][1000 genomes]
rs28496975	0.82[AFR][1000 genomes]
rs28532592	1.00[AMR][1000 genomes]
rs28699037	0.89[AFR][1000 genomes]
rs35620536	1.00[AMR][1000 genomes]
rs6509012	1.00[AMR][1000 genomes]
rs73552850	1.00[AMR][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	chr19:42775800-42781600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr19:42775800-42781800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr19:42775800-42782400	Weak transcription	Fetal Kidney	kidney
9	chr19:42775800-42783600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr19:42776000-42781200	Weak transcription	Stomach Mucosa	stomach
11	chr19:42776000-42781600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:42776200-42781800	Strong transcription	Fetal Thymus	thymus
13	chr19:42776400-42781400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
14	chr19:42776400-42782200	Genic enhancers	Pancreas	Pancrea
15	chr19:42777000-42782200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:42777200-42781400	Strong transcription	HepG2	liver
17	chr19:42777400-42781400	Strong transcription	Fetal Lung	lung
18	chr19:42777600-42781200	Genic enhancers	Liver	Liver
19	chr19:42777800-42781000	Genic enhancers	Stomach Smooth Muscle	stomach
20	chr19:42777800-42782000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:42778000-42781800	Genic enhancers	Fetal Muscle Leg	muscle
22	chr19:42778000-42783200	Genic enhancers	Placenta	Placenta
23	chr19:42778200-42781000	Genic enhancers	Gastric	stomach
24	chr19:42778200-42781400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
25	chr19:42778200-42783400	Genic enhancers	Fetal Muscle Trunk	muscle
26	chr19:42778400-42783400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:42778400-42783800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:42778600-42781000	Genic enhancers	HSMMtube	muscle
29	chr19:42778600-42781800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr19:42778600-42782000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:42778800-42781800	Genic enhancers	Muscle Satellite Cultured Cells	--
32	chr19:42778800-42781800	Genic enhancers	NHEK	skin
33	chr19:42778800-42782400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:42779000-42781200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr19:42779000-42781200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr19:42779000-42781200	Genic enhancers	Fetal Brain Male	brain
37	chr19:42779000-42783400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:42779200-42781000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr19:42779200-42781800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr19:42779200-42782000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:42779200-42783400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr19:42779200-42783400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr19:42779200-42783600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr19:42779400-42781600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:42779400-42781800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr19:42779400-42781800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:42779400-42781800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr19:42779400-42782200	Weak transcription	Ovary	ovary
49	chr19:42779400-42782400	Genic enhancers	Fetal Brain Female	brain
50	chr19:42779400-42783200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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