Variant report

Variant	rs520125
Chromosome Location	chr19:56131883-56131884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:56119724..56122187-chr19:56130812..56133496,2	K562	blood:
2	chr19:56123945..56128950-chr19:56130054..56135521,12	K562	blood:
3	chr19:56115235..56119649-chr19:56131831..56136050,11	K562	blood:
4	chr19:56109832..56113599-chr19:56126942..56132164,6	K562	blood:
5	chr19:56129094..56130603-chr19:56130975..56133243,2	K562	blood:
6	chr19:56035735..56040339-chr19:56129405..56132332,4	K562	blood:
7	chr19:56131862..56136924-chr19:56144839..56148352,5	MCF-7	breast:
8	chr19:56028711..56031331-chr19:56131776..56135542,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000179943	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000261221	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs310464	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs310465	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs310467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs310470	0.83[ASN][1000 genomes]
rs310471	0.83[ASN][1000 genomes]
rs504003	1.00[CHB][hapmap]
rs507498	1.00[CHB][hapmap]
rs522669	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs553947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs612211	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs636466	0.83[ASN][1000 genomes]
rs636467	0.83[ASN][1000 genomes]
rs637788	1.00[CHB][hapmap]
rs644230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs681433	1.00[CHB][hapmap]
rs7246799	0.83[ASN][1000 genomes]
rs889091	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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
14	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

No data

Chromatin state (count:124 , 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	chr19:56118400-56134400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:56118400-56135200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:56118400-56135200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:56118400-56135200	Weak transcription	HUVEC	blood vessel
6	chr19:56118600-56134800	Strong transcription	Fetal Intestine Small	intestine
7	chr19:56118600-56134800	Weak transcription	K562	blood
8	chr19:56118600-56135200	Weak transcription	Fetal Brain Male	brain
9	chr19:56119600-56134000	Weak transcription	HepG2	liver
10	chr19:56119600-56134800	Weak transcription	Hela-S3	cervix
11	chr19:56121200-56135000	Weak transcription	NH-A	brain
12	chr19:56121600-56134000	Strong transcription	Fetal Brain Female	brain
13	chr19:56121600-56135800	Weak transcription	NHDF-Ad	bronchial
14	chr19:56122200-56135800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:56122800-56135000	Weak transcription	HSMM	muscle
16	chr19:56123800-56134600	Strong transcription	Brain Germinal Matrix	brain
17	chr19:56124000-56132200	Weak transcription	Brain Angular Gyrus	brain
18	chr19:56124600-56132000	Weak transcription	Right Atrium	heart
19	chr19:56128400-56135600	Weak transcription	Small Intestine	intestine
20	chr19:56128600-56132600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:56129000-56133800	Weak transcription	A549	lung
22	chr19:56129000-56135000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr19:56129000-56135200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:56129200-56132000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr19:56129200-56132000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr19:56129200-56132200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr19:56129200-56132200	Weak transcription	Liver	Liver
28	chr19:56129200-56132200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr19:56129200-56132200	Weak transcription	Brain Hippocampus Middle	brain
30	chr19:56129200-56132200	Weak transcription	Duodenum Mucosa	Duodenum
31	chr19:56129200-56132400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:56129200-56132400	Weak transcription	Esophagus	oesophagus
33	chr19:56129200-56132400	Weak transcription	Gastric	stomach
34	chr19:56129200-56132400	Weak transcription	Pancreas	Pancrea
35	chr19:56129200-56132400	Weak transcription	HMEC	breast
36	chr19:56129200-56133200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr19:56129200-56133200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr19:56129200-56133600	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr19:56129200-56134400	Weak transcription	Fetal Kidney	kidney
40	chr19:56129200-56134800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr19:56129200-56134800	Weak transcription	Colon Smooth Muscle	Colon
42	chr19:56129200-56134800	Weak transcription	NHEK	skin
43	chr19:56129200-56135000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr19:56129200-56135000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr19:56129200-56135000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr19:56129200-56135000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:56129200-56135000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr19:56129200-56135000	Weak transcription	Stomach Mucosa	stomach
49	chr19:56129200-56135400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr19:56129200-56135400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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