Variant report

Variant	rs62129562
Chromosome Location	chr19:56169438-56169439
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	chr19:56169386-56170060	K562	blood:	n/a	n/a
2	POLR2A	chr19:56169187-56169470	HepG2	liver:	n/a	n/a
3	EBF1	chr19:56169306-56169673	GM12878	blood:	n/a	chr19:56169513-56169522 chr19:56169511-56169522 chr19:56169512-56169522 chr19:56169513-56169522
4	POLR2A	chr19:56169011-56170029	SK-N-MC	brain:	n/a	n/a
5	POLR2A	chr19:56169396-56169460	K562	blood:	n/a	n/a
6	WRNIP1	chr19:56166793-56170333	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:56164851-56170437	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr19:56164956-56169503	K562	blood:	n/a	n/a
9	POLR2A	chr19:56167955-56169676	GM12878	blood:	n/a	n/a
10	BHLHE40	chr19:56169355-56169615	GM12878	blood:	n/a	n/a
11	ELK1	chr19:56169400-56169567	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:56169029-56169641	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:56169127-56169602	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:54974496..54976652-chr19:56167995..56170937,2	MCF-7	breast:
2	chr19:56164666..56171824-chr19:56183341..56192911,16	MCF-7	breast:
3	chr19:56165703..56169980-chr19:56194386..56196896,5	MCF-7	breast:
4	chr19:55997140..55998839-chr19:56168520..56170217,2	MCF-7	breast:
5	chr19:56168627..56170843-chr19:56657131..56658872,2	MCF-7	breast:
6	chr19:56110428..56112493-chr19:56168408..56170811,2	MCF-7	breast:
7	chr19:54962486..54964755-chr19:56168867..56170948,2	MCF-7	breast:

Variant related genes	Relation type
U2AF2	TF binding region
ENSG00000182909	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000167685	Chromatin interaction
ENSG00000063245	Chromatin interaction
ENSG00000267523	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000211571	Chromatin interaction
ENSG00000167615	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs188701	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
5	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
6	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
7	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv833882	chr19:56158633-56326564	Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Weak transcription 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	66 gene(s)	inside rSNPs	diseases
9	nsv1061024	chr19:56167101-56217359	Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 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	chr19:56167000-56170200	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr19:56167200-56169600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr19:56167200-56169600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:56167200-56169600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr19:56167200-56169600	Flanking Active TSS	Brain Hippocampus Middle	brain
6	chr19:56167200-56169600	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
7	chr19:56167200-56170200	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
8	chr19:56167600-56169600	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
9	chr19:56167600-56170400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:56167600-56174200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:56167800-56169600	Transcr. at gene 5' and 3'	Hela-S3	cervix
12	chr19:56167800-56170200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:56167800-56170200	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr19:56167800-56170200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr19:56167800-56171400	Genic enhancers	Primary B cells from peripheral blood	blood
16	chr19:56167800-56171400	Genic enhancers	Fetal Muscle Trunk	muscle
17	chr19:56168000-56170000	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
18	chr19:56168000-56170400	Enhancers	Liver	Liver
19	chr19:56168200-56170200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
20	chr19:56168200-56170400	Genic enhancers	Fetal Muscle Leg	muscle
21	chr19:56168200-56170800	Genic enhancers	Placenta Amnion	Placenta Amnion
22	chr19:56168200-56171400	Genic enhancers	Placenta	Placenta
23	chr19:56168200-56171800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:56168200-56172400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr19:56168200-56172800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:56168400-56169600	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:56168400-56169600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr19:56168400-56169600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
29	chr19:56168400-56170200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr19:56168600-56169600	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr19:56168600-56169600	Enhancers	HSMMtube	muscle
32	chr19:56168600-56169800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:56168600-56170000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr19:56168600-56170200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr19:56168600-56170200	Genic enhancers	Fetal Stomach	stomach
36	chr19:56168600-56170400	Genic enhancers	Fetal Intestine Small	intestine
37	chr19:56168600-56170400	Enhancers	Fetal Lung	lung
38	chr19:56168600-56170800	Enhancers	Fetal Heart	heart
39	chr19:56168600-56171200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:56168600-56172200	Genic enhancers	Spleen	Spleen
41	chr19:56168800-56169600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
42	chr19:56168800-56169800	Enhancers	Primary hematopoietic stem cells	blood
43	chr19:56168800-56170000	Enhancers	Primary B cells from cord blood	blood
44	chr19:56168800-56170400	Enhancers	H1 Cell Line	embryonic stem cell
45	chr19:56168800-56170400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
46	chr19:56168800-56170600	Enhancers	Stomach Mucosa	stomach
47	chr19:56168800-56170800	Enhancers	Ovary	ovary
48	chr19:56168800-56171000	Enhancers	Brain Substantia Nigra	brain
49	chr19:56169000-56169600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr19:56169000-56169600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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