Variant report

Variant	rs7249342
Chromosome Location	chr19:52899450-52899451
allele	C/T
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	CTCF	chr19:52899422-52899524	Lung_OC	lung:	n/a	n/a

Variant related genes	Relation type
ZNF528	TF binding region
ENSG00000269834	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10401152	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11883016	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs162121	1.00[EUR][1000 genomes]
rs162122	1.00[EUR][1000 genomes]
rs2560994	1.00[EUR][1000 genomes]
rs2608512	1.00[EUR][1000 genomes]
rs2608516	1.00[EUR][1000 genomes]
rs324090	1.00[EUR][1000 genomes]
rs324109	1.00[EUR][1000 genomes]
rs7252819	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	esv3401193	chr19:52818960-52909749	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv912300	chr19:52832830-52928039	Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv912301	chr19:52835210-52914233	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv912302	chr19:52859828-52928039	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv2536	chr19:52869457-52902064	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv912303	chr19:52874140-52928039	ZNF genes & repeats Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	esv3372061	chr19:52877189-52902218	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv521079	chr19:52886137-52917626	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv828615	chr19:52888767-52936555	ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
13	esv2762048	chr19:52895166-52997571	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52889200-52900800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr19:52891200-52899600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
3	chr19:52891600-52899800	ZNF genes & repeats	Fetal Brain Female	brain
4	chr19:52893400-52900200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr19:52893800-52899600	Weak transcription	Right Ventricle	heart
6	chr19:52894000-52900000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:52895600-52900400	ZNF genes & repeats	Fetal Stomach	stomach
8	chr19:52896400-52900200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:52896600-52900400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:52896800-52900200	ZNF genes & repeats	Fetal Lung	lung
11	chr19:52896800-52900400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr19:52896800-52900600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:52897200-52900400	ZNF genes & repeats	Fetal Muscle Leg	muscle
14	chr19:52897400-52899600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:52897400-52899600	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr19:52897400-52899800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
17	chr19:52897400-52899800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr19:52897400-52900000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr19:52897400-52900000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:52897400-52900000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr19:52897400-52900200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
22	chr19:52897400-52900200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
23	chr19:52897400-52900200	ZNF genes & repeats	Ovary	ovary
24	chr19:52897400-52900400	ZNF genes & repeats	Liver	Liver
25	chr19:52897400-52900400	ZNF genes & repeats	Fetal Intestine Small	intestine
26	chr19:52897400-52900600	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr19:52897600-52899800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr19:52897600-52900000	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr19:52897600-52900200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:52897600-52900200	ZNF genes & repeats	Fetal Kidney	kidney
31	chr19:52897600-52900200	ZNF genes & repeats	Spleen	Spleen
32	chr19:52897600-52900400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:52897600-52900400	ZNF genes & repeats	Primary B cells from cord blood	blood
34	chr19:52897600-52900400	ZNF genes & repeats	Lung	lung
35	chr19:52897600-52901000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
36	chr19:52897800-52899600	Strong transcription	Left Ventricle	heart
37	chr19:52897800-52899600	Strong transcription	Osteobl	bone
38	chr19:52897800-52900000	ZNF genes & repeats	Brain Germinal Matrix	brain
39	chr19:52897800-52900000	Weak transcription	Psoas Muscle	Psoas
40	chr19:52898000-52899600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr19:52898000-52900200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
42	chr19:52898000-52900200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
43	chr19:52898000-52900400	ZNF genes & repeats	Fetal Intestine Large	intestine
44	chr19:52898000-52900400	ZNF genes & repeats	Rectal Smooth Muscle	rectum
45	chr19:52898000-52902200	ZNF genes & repeats	Placenta	Placenta
46	chr19:52898000-52902800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:52898200-52900000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
48	chr19:52898200-52900200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr19:52898200-52900200	ZNF genes & repeats	HSMMtube	muscle
50	chr19:52898200-52900400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood

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