Variant report

Variant	rs3745099
Chromosome Location	chr19:52901905-52901906
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	MXI1	chr19:52900596-52902332	SK-N-SH	brain:	n/a	n/a
2	GABPA	chr19:52900745-52901930	SK-N-SH	brain:	n/a	n/a
3	REST	chr19:52900741-52902049	H1-neurons	neurons:	n/a	chr19:52901216-52901226 chr19:52901249-52901262

No.	Distal block	Cell Line	Cell type
1	chr19:52839189..52842101-chr19:52900021..52902093,2	MCF-7	breast:
2	chr19:52893005..52896642-chr19:52900305..52903556,3	MCF-7	breast:
3	chr19:52771349..52773088-chr19:52900874..52902470,2	MCF-7	breast:
4	chr19:52901728..52903647-chr19:52912630..52914410,2	MCF-7	breast:
5	chr19:52899758..52902696-chr19:52903314..52905986,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269834	TF binding region
ZNF528	TF binding region
ENSG00000167555	Chromatin interaction
ENSG00000196214	Chromatin interaction
ENSG00000167554	Chromatin interaction
ENSG00000269834	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs150990	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2059816	0.83[EUR][1000 genomes]
rs2608515	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs324091	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes];0.87[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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52898000-52902200	ZNF genes & repeats	Placenta	Placenta
2	chr19:52898000-52902800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr19:52898200-52903600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
4	chr19:52900000-52902000	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr19:52900000-52902000	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:52900000-52902000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
7	chr19:52900000-52902000	Active TSS	NHLF	lung
8	chr19:52900200-52902000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:52900200-52902000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr19:52900200-52902000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:52900200-52902000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:52900200-52902000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr19:52900200-52902200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
14	chr19:52900200-52902200	Active TSS	iPS-15b Cell Line	embryonic stem cell
15	chr19:52900200-52902200	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr19:52900200-52902200	ZNF genes & repeats	GM12878-XiMat	blood
17	chr19:52900200-52902200	Active TSS	HSMMtube	muscle
18	chr19:52900200-52902400	Active TSS	NH-A	brain
19	chr19:52900400-52902000	Active TSS	H9 Cell Line	embryonic stem cell
20	chr19:52900400-52902000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr19:52900400-52902000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:52900400-52902200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:52900400-52902200	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr19:52900400-52902200	Active TSS	Rectal Smooth Muscle	rectum
25	chr19:52900600-52902000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
26	chr19:52900600-52902000	Active TSS	Fetal Intestine Large	intestine
27	chr19:52900600-52902000	Active TSS	K562	blood
28	chr19:52900600-52902200	Active TSS	HSMM	muscle
29	chr19:52900800-52902000	Active TSS	Placenta Amnion	Placenta Amnion
30	chr19:52900800-52902200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:52900800-52902200	Active TSS	Osteobl	bone
32	chr19:52901200-52902000	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr19:52901200-52902000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr19:52901200-52902000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:52901200-52902000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
36	chr19:52901200-52902000	Bivalent/Poised TSS	HepG2	liver
37	chr19:52901200-52902200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:52901400-52902000	Flanking Active TSS	Primary B cells from cord blood	blood
39	chr19:52901400-52902000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:52901400-52902000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr19:52901400-52902000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
42	chr19:52901400-52902000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr19:52901400-52902000	Flanking Active TSS	Fetal Muscle Trunk	muscle
44	chr19:52901400-52902000	Flanking Active TSS	Right Ventricle	heart
45	chr19:52901400-52902000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr19:52901400-52902000	Flanking Active TSS	NHEK	skin
47	chr19:52901400-52902200	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr19:52901400-52902200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr19:52901400-52902200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr19:52901400-52902200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

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