Variant report

Variant	rs12978696
Chromosome Location	chr19:56895496-56895497
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	NFIC	chr19:56895121-56895505	ECC-1	luminal epithelium:	n/a	n/a
2	NFIC	chr19:56895000-56896031	ECC-1	luminal epithelium:	n/a	n/a
3	TEAD4	chr19:56895173-56896091	ECC-1	luminal epithelium:	n/a	n/a
4	TEAD4	chr19:56895117-56896128	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr19:56895458-56896030	ECC-1	luminal epithelium:	n/a	n/a
6	EP300	chr19:56895139-56896180	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:56895475..56897823-chr19:56903707..56905886,2	K562	blood:

Variant related genes	Relation type
SLC25A36P1	TF binding region
ENSG00000267192	TF binding region
ENSG00000018869	Chromatin interaction
ENSG00000267454	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1017102	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12608563	0.83[ASN][1000 genomes]
rs12610246	0.83[ASN][1000 genomes]
rs12610899	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12981331	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12983342	0.91[ASN][1000 genomes]
rs2304123	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304125	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2304126	0.83[ASN][1000 genomes]
rs2304127	0.94[ASN][1000 genomes]
rs8111942	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56881200-56904000	ZNF genes & repeats	Liver	Liver
2	chr19:56889200-56897400	Weak transcription	Gastric	stomach
3	chr19:56889200-56901200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:56889200-56904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:56889400-56895600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:56889400-56904000	Weak transcription	Fetal Heart	heart
7	chr19:56889400-56904000	Weak transcription	K562	blood
8	chr19:56890000-56900200	Weak transcription	Right Ventricle	heart
9	chr19:56890200-56903600	Weak transcription	Fetal Brain Male	brain
10	chr19:56890600-56900200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:56890600-56900400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr19:56890600-56904000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:56890800-56895600	Weak transcription	Left Ventricle	heart
14	chr19:56893200-56896400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:56893600-56899800	Weak transcription	Placenta	Placenta
16	chr19:56893600-56900000	Weak transcription	Pancreas	Pancrea
17	chr19:56894200-56895600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr19:56894200-56897600	ZNF genes & repeats	Adipose Nuclei	Adipose
19	chr19:56894200-56899000	Weak transcription	Fetal Intestine Large	intestine
20	chr19:56894200-56900800	ZNF genes & repeats	Primary T cells from cord blood	blood
21	chr19:56894200-56903800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:56894400-56896000	Strong transcription	Brain Inferior Temporal Lobe	brain
23	chr19:56894400-56896000	ZNF genes & repeats	Fetal Lung	lung
24	chr19:56894400-56897000	ZNF genes & repeats	NHEK	skin
25	chr19:56894400-56898200	ZNF genes & repeats	Ovary	ovary
26	chr19:56894400-56898400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr19:56894400-56899000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
28	chr19:56894600-56896800	ZNF genes & repeats	Fetal Kidney	kidney
29	chr19:56894600-56899800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr19:56894800-56896600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
31	chr19:56894800-56897800	Strong transcription	Brain Cingulate Gyrus	brain
32	chr19:56894800-56898000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:56894800-56900000	Weak transcription	Fetal Stomach	stomach
34	chr19:56894800-56902000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr19:56894800-56902000	Strong transcription	Brain Hippocampus Middle	brain
36	chr19:56894800-56903400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr19:56895000-56896400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
38	chr19:56895000-56896800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr19:56895000-56896800	Strong transcription	Brain Anterior Caudate	brain
40	chr19:56895000-56897000	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr19:56895000-56897800	Strong transcription	Brain Germinal Matrix	brain
42	chr19:56895000-56898000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:56895000-56898600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
44	chr19:56895200-56895800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
45	chr19:56895200-56896000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
46	chr19:56895200-56896000	Strong transcription	Brain Angular Gyrus	brain
47	chr19:56895200-56896400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
48	chr19:56895200-56896600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
49	chr19:56895200-56896600	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:56895200-56896800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood

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