Variant report

Variant	rs13347002
Chromosome Location	chr19:41307927-41307928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:38)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:38 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41307602-41308421	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:41307829-41308541	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr19:41307704-41308359	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:41307777-41308322	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:41307677-41309301	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr19:41307872-41308289	A549	lung:	n/a	n/a
7	POLR2A	chr19:41307782-41308337	A549	lung:	n/a	n/a
8	POLR2A	chr19:41307692-41309535	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr19:41307763-41308093	GM12891	blood:	n/a	n/a
10	HEY1	chr19:41307740-41308372	K562	blood:	n/a	n/a
11	POLR2A	chr19:41307635-41308378	K562	blood:	n/a	n/a
12	POLR2A	chr19:41307772-41308356	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:41307762-41308167	Hela-S3	cervix:	n/a	n/a
14	MAX	chr19:41307697-41307954	K562	blood:	n/a	n/a
15	PML	chr19:41307763-41308168	K562	blood:	n/a	n/a
16	POLR2A	chr19:41307698-41308404	GM12891	blood:	n/a	n/a
17	POLR2A	chr19:41307718-41308304	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr19:41307763-41308357	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr19:41307117-41318353	K562	blood:	n/a	n/a
20	POLR2A	chr19:41307663-41316128	GM12892	blood:	n/a	n/a
21	POLR2A	chr19:41307717-41308380	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr19:41307696-41309307	GM12891	blood:	n/a	n/a
23	POLR2A	chr19:41307671-41311968	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:41307742-41308421	GM12892	blood:	n/a	n/a
25	POLR2A	chr19:41307768-41311357	K562	blood:	n/a	n/a
26	POLR2A	chr19:41307876-41312060	HepG2	liver:	n/a	n/a
27	POLR2A	chr19:41307781-41314972	GM12891	blood:	n/a	n/a
28	POLR2A	chr19:41307714-41308392	HL-60	blood:	n/a	n/a
29	POLR2A	chr19:41307841-41308307	HepG2	liver:	n/a	n/a
30	POLR2A	chr19:41307925-41307973	MCF-7	breast:	n/a	n/a
31	POLR2A	chr19:41307556-41311130	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:41307847-41308315	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr19:41307797-41308328	A549	lung:	n/a	n/a
34	POLR2A	chr19:41307706-41308399	K562	blood:	n/a	n/a
35	POLR2A	chr19:41307711-41308421	GM12878	blood:	n/a	n/a
36	POLR2A	chr19:41307640-41313313	K562	blood:	n/a	n/a
37	POLR2A	chr19:41307839-41311076	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:41307706-41308363	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41220581..41222873-chr19:41307320..41309933,2	MCF-7	breast:
2	chr19:41254487..41259247-chr19:41302579..41309995,18	K562	blood:
3	chr19:41266506..41270324-chr19:41304182..41308237,4	MCF-7	breast:
4	chr19:41281718..41286533-chr19:41301356..41311124,20	K562	blood:
5	chr19:41307021..41309215-chr19:41770332..41772001,2	MCF-7	breast:
6	chr19:41220369..41226479-chr19:41305318..41310706,7	K562	blood:
7	chr19:41253776..41259894-chr19:41301950..41310086,19	MCF-7	breast:
8	chr19:41283422..41285801-chr19:41305183..41308009,2	MCF-7	breast:
9	chr19:41115624..41118176-chr19:41306706..41309360,2	MCF-7	breast:
10	chr19:41253887..41263110-chr19:41303366..41316425,33	K562	blood:

No data

Variant related genes	Relation type
EGLN2	TF binding region
ENSG00000171570	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000077312	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000123815	Chromatin interaction
ENSG00000086544	Chromatin interaction
ENSG00000261857	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10402565	1.00[AMR][1000 genomes]
rs10405792	1.00[AMR][1000 genomes]
rs10408452	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs10415973	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10417139	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10420158	1.00[AMR][1000 genomes]
rs10422086	1.00[AMR][1000 genomes]
rs10422737	1.00[AMR][1000 genomes]
rs11083594	1.00[AMR][1000 genomes]
rs12104289	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs13345967	1.00[AMR][1000 genomes]
rs28368968	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28609092	1.00[AMR][1000 genomes]
rs28636772	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758500	chr19:41291627-41546068	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2758762	chr19:41291627-41546068	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41305800-41309000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41305800-41316200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:41306000-41308400	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
4	chr19:41306000-41308800	Transcr. at gene 5' and 3'	A549	lung
5	chr19:41306000-41309000	Transcr. at gene 5' and 3'	Placenta	Placenta
6	chr19:41306000-41309200	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr19:41306000-41309200	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
8	chr19:41306000-41310400	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
9	chr19:41306000-41311800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:41306200-41308200	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr19:41306200-41308400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:41306200-41308600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
13	chr19:41306200-41308800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr19:41306200-41308800	Transcr. at gene 5' and 3'	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:41306200-41309000	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:41306200-41309200	Transcr. at gene 5' and 3'	NHLF	lung
17	chr19:41306200-41309400	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
18	chr19:41306200-41309600	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
19	chr19:41306200-41309800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
20	chr19:41306200-41309800	Transcr. at gene 5' and 3'	Dnd41	blood
21	chr19:41306200-41310200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:41306200-41311200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
23	chr19:41306200-41313200	Enhancers	Fetal Heart	heart
24	chr19:41306400-41308000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:41306400-41308200	Genic enhancers	Liver	Liver
26	chr19:41306400-41308200	Transcr. at gene 5' and 3'	Brain Inferior Temporal Lobe	brain
27	chr19:41306400-41308200	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
28	chr19:41306400-41308200	Transcr. at gene 5' and 3'	Right Ventricle	heart
29	chr19:41306400-41308200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
30	chr19:41306400-41308400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:41306400-41308600	Genic enhancers	Placenta Amnion	Placenta Amnion
32	chr19:41306400-41308600	Enhancers	Stomach Mucosa	stomach
33	chr19:41306400-41308800	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
34	chr19:41306400-41309200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:41306400-41309200	Transcr. at gene 5' and 3'	Osteobl	bone
36	chr19:41306400-41309800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:41306400-41310000	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
38	chr19:41306400-41311200	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
39	chr19:41306400-41313600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:41306400-41313800	Genic enhancers	Fetal Thymus	thymus
41	chr19:41306400-41316200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:41306400-41316800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr19:41306600-41308000	Strong transcription	Aorta	Aorta
44	chr19:41306600-41308200	Genic enhancers	Primary monocytes fromperipheralblood	blood
45	chr19:41306600-41308200	Genic enhancers	Primary B cells from peripheral blood	blood
46	chr19:41306600-41308200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
47	chr19:41306600-41308400	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
48	chr19:41306600-41309200	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:41306600-41309200	Transcr. at gene 5' and 3'	Brain Hippocampus Middle	brain
50	chr19:41306600-41309200	Transcr. at gene 5' and 3'	HSMM	muscle

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