Variant report

Variant	rs57689442
Chromosome Location	chr19:39928497-39928498
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4G	chr19:39928468-39928711	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
3	HNF4A	chr19:39928385-39928665	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:39928355-39928601	HCT-116	colon:	n/a	n/a
5	POLR2A	chr19:39928323-39928691	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr19:39928316-39928645	ECC-1	luminal epithelium:	n/a	n/a
8	SIN3AK20	chr19:39913141-39929158	PANC-1	pancreas:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39832709..39837239-chr19:39925090..39928725,4	K562	blood:
2	chr19:39619125..39620938-chr19:39926907..39929414,2	K562	blood:
3	chr19:39926650..39928509-chr19:39969774..39972138,2	MCF-7	breast:
4	chr17:57919100..57920854-chr19:39926824..39928779,2	MCF-7	breast:
5	chr19:39924469..39929022-chr19:39934307..39938518,21	MCF-7	breast:
6	chr19:39925083..39928891-chr19:40028576..40030872,3	K562	blood:

No data

Variant related genes	Relation type
RPS16	TF binding region
SUPT5H	TF binding region
ENSG00000213922	TF binding region
ENSG00000105197	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000176396	Chromatin interaction
ENSG00000196235	Chromatin interaction
ENSG00000130755	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs507512	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61639559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61676286	1.00[AMR][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	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
3	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 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	chr19:39926600-39935200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:39927400-39928600	Enhancers	Fetal Muscle Trunk	muscle
3	chr19:39927400-39928800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr19:39927400-39929800	Enhancers	Placenta	Placenta
5	chr19:39927400-39930200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:39927400-39930400	Weak transcription	K562	blood
7	chr19:39927400-39930800	Weak transcription	Brain Angular Gyrus	brain
8	chr19:39927400-39935200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:39927400-39935200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:39927400-39935200	Weak transcription	Gastric	stomach
11	chr19:39927400-39935200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr19:39927600-39928600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr19:39927600-39928800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:39927600-39928800	Enhancers	Fetal Intestine Large	intestine
15	chr19:39927600-39929200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:39927600-39929200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr19:39927600-39929400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:39927600-39930200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr19:39927600-39930200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr19:39927600-39930600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:39927600-39930600	Weak transcription	GM12878-XiMat	blood
22	chr19:39927600-39930800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr19:39927600-39930800	Weak transcription	Brain Hippocampus Middle	brain
24	chr19:39927600-39930800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr19:39927600-39930800	Weak transcription	Fetal Heart	heart
26	chr19:39927600-39931000	Weak transcription	Primary B cells from cord blood	blood
27	chr19:39927600-39931000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr19:39927600-39931000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr19:39927600-39931000	Weak transcription	Liver	Liver
30	chr19:39927600-39931000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr19:39927600-39931000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr19:39927600-39932000	Enhancers	A549	lung
33	chr19:39927600-39934800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:39927600-39935000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr19:39927600-39935000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr19:39927600-39935000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:39927600-39935000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr19:39927600-39935000	Weak transcription	HMEC	breast
39	chr19:39927600-39935200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr19:39927600-39935200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr19:39927600-39935200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr19:39927600-39935200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr19:39927600-39935200	Weak transcription	Brain Anterior Caudate	brain
44	chr19:39927600-39935200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr19:39927600-39935200	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr19:39927600-39935200	Weak transcription	Fetal Kidney	kidney
47	chr19:39927600-39935200	Weak transcription	HSMMtube	muscle
48	chr19:39927600-39935200	Weak transcription	NHLF	lung
49	chr19:39927800-39928600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr19:39927800-39928600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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