Variant report

Variant	rs12608801
Chromosome Location	chr19:23599127-23599128
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	REST	chr19:23597834-23599167	H1-neurons	neurons:	n/a	chr19:23598539-23598552 chr19:23598583-23598596 chr19:23598478-23598496 chr19:23598480-23598493
2	POLR2A	chr19:23597581-23599267	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr19:23597730-23599261	SK-N-SH	brain:	n/a	n/a
4	TAF1	chr19:23597882-23599239	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:23597107..23600085-chr19:24215651..24217575,2	MCF-7	breast:
2	chr19:23597097..23600084-chr19:24215418..24217838,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269416	TF binding region
ENSG00000268362	Chromatin interaction
ENSG00000213096	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12609284	0.83[ASN][1000 genomes]
rs12609333	0.94[ASN][1000 genomes]
rs12610986	0.90[ASN][1000 genomes]
rs293899	0.83[ASN][1000 genomes]
rs293902	0.83[ASN][1000 genomes]
rs295354	0.83[ASN][1000 genomes]
rs295397	0.87[ASN][1000 genomes]
rs295417	0.83[ASN][1000 genomes]
rs296079	0.85[ASN][1000 genomes]
rs35833976	0.82[ASN][1000 genomes]
rs405145	0.81[ASN][1000 genomes]
rs422044	0.83[ASN][1000 genomes]
rs59863959	0.87[ASN][1000 genomes]
rs606928	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34470	chr19:22922549-23659458	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
2	esv34907	chr19:22922549-23683097	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
3	nsv9686	chr19:22989454-23653750	Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
4	nsv817826	chr19:23000745-23620632	Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	esv3693269	chr19:23000745-23652839	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
6	esv2758491	chr19:23071299-23940467	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1065157	chr19:23091826-23812323	Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
8	nsv543959	chr19:23091826-23812323	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
9	nsv579034	chr19:23387788-23610784	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	esv3447830	chr19:23465035-23610690	Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
11	esv3382338	chr19:23476728-23631356	Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
12	esv3323302	chr19:23477342-23648545	ZNF genes & repeats Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	esv3523857	chr19:23477614-23632199	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
14	esv3523858	chr19:23477614-23632199	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
15	esv3334120	chr19:23545829-23837686	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
16	nsv960817	chr19:23556437-23606658	ZNF genes & repeats Genic enhancers Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1064929	chr19:23559483-23827735	Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
18	nsv1057474	chr19:23563612-23812441	ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
19	nsv543962	chr19:23563612-23812441	ZNF genes & repeats Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
20	esv3334156	chr19:23590778-23742435	Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv1060263	chr19:23592291-23660609	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv1065071	chr19:23596756-23660609	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
23	nsv1057958	chr19:23596756-24159379	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
24	nsv543963	chr19:23596756-24159379	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:23596800-23599600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr19:23597200-23599200	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr19:23597400-23599200	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr19:23597400-23599200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr19:23597400-23599200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr19:23597400-23599200	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr19:23597400-23599400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:23597600-23599200	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr19:23597600-23599200	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr19:23597600-23599200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:23597600-23599200	Bivalent/Poised TSS	Primary hematopoietic stem cells	blood
12	chr19:23597600-23599200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:23597600-23599200	Active TSS	Brain Germinal Matrix	brain
14	chr19:23597600-23599200	Active TSS	Fetal Brain Female	brain
15	chr19:23597600-23599400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr19:23597600-23599400	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr19:23597800-23599200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:23597800-23599200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:23597800-23599200	Active TSS	Fetal Heart	heart
20	chr19:23598000-23599200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
21	chr19:23598000-23599200	Active TSS	NHDF-Ad	bronchial
22	chr19:23598200-23599200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr19:23598200-23599200	Active TSS	Fetal Brain Male	brain
24	chr19:23598200-23599400	Flanking Active TSS	Duodenum Mucosa	Duodenum
25	chr19:23598400-23599200	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr19:23598400-23599400	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:23598600-23599200	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr19:23598800-23599200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr19:23598800-23599200	Active TSS	Brain Hippocampus Middle	brain
30	chr19:23598800-23599200	Enhancers	Gastric	stomach
31	chr19:23598800-23599200	Active TSS	Right Ventricle	heart
32	chr19:23599000-23599200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
33	chr19:23599000-23599200	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr19:23599000-23599200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr19:23599000-23599200	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr19:23599000-23599200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr19:23599000-23599200	Bivalent Enhancer	Adipose Nuclei	Adipose
38	chr19:23599000-23599200	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr19:23599000-23599200	Flanking Active TSS	Fetal Intestine Small	intestine
40	chr19:23599000-23599200	Flanking Active TSS	Fetal Kidney	kidney
41	chr19:23599000-23599200	Enhancers	Fetal Lung	lung
42	chr19:23599000-23599200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr19:23599000-23599200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
44	chr19:23599000-23599400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr19:23599000-23599400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr19:23599000-23599400	Enhancers	Stomach Mucosa	stomach
47	chr19:23599000-23599600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood

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