Variant report

Variant	rs3852898
Chromosome Location	chr19:56127597-56127598
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:56091961..56094191-chr19:56125240..56128185,2	K562	blood:
2	chr19:56123945..56128950-chr19:56130054..56135521,12	K562	blood:
3	chr19:56116288..56120130-chr19:56126715..56130598,5	MCF-7	breast:
4	chr19:56122149..56126669-chr19:56127522..56130662,5	MCF-7	breast:
5	chr19:56109832..56113599-chr19:56126942..56132164,6	K562	blood:
6	chr19:56125664..56128037-chr19:56135506..56137202,2	MCF-7	breast:
7	chr19:56125033..56127900-chr19:56132851..56135429,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000179922	Chromatin interaction
ENSG00000218891	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000171443	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12460543	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2280254	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292810	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2292811	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34318926	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34907477	0.87[ASN][1000 genomes]
rs35763366	0.81[EUR][1000 genomes]
rs57314044	0.86[ASN][1000 genomes]
rs751729	0.89[ASN][1000 genomes]
rs8110652	0.87[ASN][1000 genomes]
rs908668	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	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
9	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	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
12	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
13	nsv912502	chr19:56099884-56138575	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56118200-56135000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr19:56118400-56128800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr19:56118400-56134400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:56118400-56135200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:56118400-56135200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:56118400-56135200	Weak transcription	HUVEC	blood vessel
7	chr19:56118600-56128800	Weak transcription	Stomach Mucosa	stomach
8	chr19:56118600-56129600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:56118600-56129800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:56118600-56131600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr19:56118600-56131800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:56118600-56134800	Strong transcription	Fetal Intestine Small	intestine
13	chr19:56118600-56134800	Weak transcription	K562	blood
14	chr19:56118600-56135200	Weak transcription	Fetal Brain Male	brain
15	chr19:56118800-56127600	Weak transcription	HMEC	breast
16	chr19:56118800-56129400	Strong transcription	Thymus	Thymus
17	chr19:56118800-56131000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr19:56119600-56134000	Weak transcription	HepG2	liver
19	chr19:56119600-56134800	Weak transcription	Hela-S3	cervix
20	chr19:56120200-56129400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:56120400-56129400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:56120800-56129200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:56120800-56129400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr19:56121000-56129200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:56121200-56135000	Weak transcription	NH-A	brain
26	chr19:56121400-56127600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:56121400-56129400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr19:56121400-56129800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:56121600-56129600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr19:56121600-56130600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr19:56121600-56131600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr19:56121600-56134000	Strong transcription	Fetal Brain Female	brain
33	chr19:56121600-56135800	Weak transcription	NHDF-Ad	bronchial
34	chr19:56121800-56128800	Weak transcription	Fetal Kidney	kidney
35	chr19:56121800-56130400	Strong transcription	Fetal Stomach	stomach
36	chr19:56122200-56135800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:56122600-56128800	Weak transcription	A549	lung
38	chr19:56122800-56135000	Weak transcription	HSMM	muscle
39	chr19:56123000-56129400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:56123400-56129200	Strong transcription	Stomach Smooth Muscle	stomach
41	chr19:56123400-56129600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr19:56123600-56128800	Weak transcription	Primary T cells from cord blood	blood
43	chr19:56123800-56134600	Strong transcription	Brain Germinal Matrix	brain
44	chr19:56124000-56128200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:56124000-56128600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:56124000-56129200	Strong transcription	Dnd41	blood
47	chr19:56124000-56129600	Strong transcription	Fetal Muscle Leg	muscle
48	chr19:56124000-56132200	Weak transcription	Brain Angular Gyrus	brain
49	chr19:56124200-56129200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr19:56124600-56128200	Strong transcription	Primary neutrophils fromperipheralblood	blood

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