Variant report

Variant	rs56138629
Chromosome Location	chr19:39883988-39883989
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	POLR2A	chr19:39850716-39886400	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39832559..39836457-chr19:39880660..39884768,5	MCF-7	breast:
2	chr19:39881608..39883265-chr19:39883392..39885863,2	MCF-7	breast:

Variant related genes	Relation type
PAF1	TF binding region
ENSG00000006712	Chromatin interaction
ENSG00000179134	Chromatin interaction
ENSG00000063322	Chromatin interaction
ENSG00000269246	Chromatin interaction
ENSG00000130755	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1057745	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12459135	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58587357	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911679	chr19:39735106-39924129	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	198 gene(s)	inside rSNPs	diseases
2	nsv1058514	chr19:39744112-39902580	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv911680	chr19:39792460-39924129	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	194 gene(s)	inside rSNPs	diseases
4	esv10629	chr19:39811570-39886212	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	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
6	nsv911682	chr19:39847132-39914748	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
7	nsv911683	chr19:39847132-39924129	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	185 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39882400-39884200	Weak transcription	Gastric	stomach
2	chr19:39882400-39884200	Weak transcription	Stomach Mucosa	stomach
3	chr19:39883000-39884000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr19:39883000-39884000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr19:39883000-39884200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr19:39883000-39884200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:39883000-39884200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr19:39883000-39884200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr19:39883000-39884200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr19:39883000-39884200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr19:39883000-39884200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:39883000-39884200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr19:39883000-39884200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr19:39883000-39884200	Weak transcription	Aorta	Aorta
15	chr19:39883000-39884200	Weak transcription	Esophagus	oesophagus
16	chr19:39883000-39884200	Weak transcription	Left Ventricle	heart
17	chr19:39883000-39884200	Weak transcription	Lung	lung
18	chr19:39883000-39884200	Weak transcription	Ovary	ovary
19	chr19:39883000-39884200	Weak transcription	Pancreas	Pancrea
20	chr19:39883000-39884200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr19:39883000-39884200	Weak transcription	HSMMtube	muscle
22	chr19:39883000-39884200	Weak transcription	NH-A	brain
23	chr19:39883000-39888000	Weak transcription	Psoas Muscle	Psoas
24	chr19:39883000-39888200	Weak transcription	Right Atrium	heart
25	chr19:39883000-39888600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr19:39883000-39888600	Weak transcription	Small Intestine	intestine
27	chr19:39883000-39891800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:39883200-39884000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr19:39883200-39884000	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr19:39883200-39884000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:39883200-39884000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr19:39883200-39884000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr19:39883200-39884000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr19:39883200-39884000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:39883200-39884000	Weak transcription	Adipose Nuclei	Adipose
36	chr19:39883200-39884000	Weak transcription	Fetal Intestine Large	intestine
37	chr19:39883200-39884000	Weak transcription	Spleen	Spleen
38	chr19:39883200-39884000	Weak transcription	A549	lung
39	chr19:39883200-39884000	Enhancers	Dnd41	blood
40	chr19:39883200-39884000	Weak transcription	GM12878-XiMat	blood
41	chr19:39883200-39884000	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr19:39883200-39884200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr19:39883200-39884200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr19:39883200-39884200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr19:39883200-39884200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:39883200-39884200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:39883200-39884200	Weak transcription	Brain Angular Gyrus	brain
48	chr19:39883200-39884200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:39883200-39884200	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr19:39883200-39884200	Weak transcription	Brain Substantia Nigra	brain

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