Variant report

Variant	rs62113350
Chromosome Location	chr19:52096677-52096678
allele	C/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	JUND	chr19:52096581-52096691	HepG2	liver:	n/a	chr19:52096653-52096662
2	POLR2A	chr19:52096638-52096705	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:52096649-52098159	GM12878	blood:	n/a	n/a
4	POLR2A	chr19:52095177-52098004	U87	brain:	n/a	n/a
5	POLR2A	chr19:52095947-52098295	K562	blood:	n/a	n/a
6	POLR2A	chr19:52095284-52097348	U87	brain:	n/a	n/a
7	GATA2	chr19:52096634-52097472	HUVEC	blood vessel:	n/a	chr19:52096856-52096877 chr19:52096863-52096872 chr19:52097058-52097074 chr19:52096859-52096875 chr19:52096862-52096872 chr19:52097056-52097077 chr19:52096863-52096870 chr19:52096833-52096840 chr19:52097060-52097074
8	POLR2A	chr19:52095276-52097905	K562	blood:	n/a	n/a
9	POLR2A	chr19:52095284-52097962	U87	brain:	n/a	n/a
10	POLR2A	chr19:52096111-52097902	GM12878	blood:	n/a	n/a
11	POLR2A	chr19:52096002-52096926	K562	blood:	n/a	n/a
12	POLR2A	chr19:52096541-52098016	GM12891	blood:	n/a	n/a
13	MYC	chr19:52096543-52096678	MCF-7	breast:	n/a	n/a
14	POLR2A	chr19:52096408-52096871	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr19:52095171-52098010	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:51914893..51917429-chr19:52094517..52097128,3	K562	blood:
2	chr19:52095454..52097791-chr19:52104410..52105932,2	K562	blood:
3	chr19:51869850..51871538-chr19:52096656..52099033,2	K562	blood:
4	chr19:52096005..52097791-chr19:52103717..52105932,2	K562	blood:
5	chr19:51897297..51899400-chr19:52095029..52099296,3	K562	blood:
6	chr19:52073066..52077206-chr19:52096074..52099799,4	K562	blood:

Variant related genes	Relation type
ENSG00000269388	TF binding region
ENSG00000105497	Chromatin interaction
ENSG00000268889	Chromatin interaction
ENSG00000269388	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000269403	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10412978	0.89[ASN][1000 genomes]
rs10500308	0.80[EUR][1000 genomes]
rs11672358	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12979133	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62114988	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases
8	nsv579966	chr19:52075622-52131119	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
10	nsv9740	chr19:52096231-52107021	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52075800-52096800	Weak transcription	HepG2	liver
2	chr19:52077000-52097000	Weak transcription	Hela-S3	cervix
3	chr19:52091200-52096800	Weak transcription	Small Intestine	intestine
4	chr19:52091400-52096800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:52091400-52096800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:52091400-52096800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:52091600-52096800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:52091600-52097000	Weak transcription	Aorta	Aorta
9	chr19:52091800-52096800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr19:52091800-52096800	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:52091800-52096800	Weak transcription	NHLF	lung
12	chr19:52091800-52097000	Weak transcription	Fetal Lung	lung
13	chr19:52091800-52097000	Weak transcription	Osteobl	bone
14	chr19:52092000-52096800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr19:52092000-52096800	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr19:52092000-52096800	Weak transcription	HSMMtube	muscle
17	chr19:52092000-52097000	Weak transcription	HUVEC	blood vessel
18	chr19:52092600-52096800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr19:52095800-52096800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr19:52096000-52097000	Enhancers	Placenta	Placenta
21	chr19:52096200-52096800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr19:52096200-52096800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr19:52096200-52096800	Enhancers	Gastric	stomach
24	chr19:52096200-52097000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr19:52096200-52097000	Enhancers	Lung	lung
26	chr19:52096200-52097000	Enhancers	Spleen	Spleen
27	chr19:52096200-52097200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:52096400-52096800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:52096400-52096800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr19:52096400-52096800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr19:52096400-52096800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr19:52096400-52096800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:52096400-52096800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr19:52096400-52096800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr19:52096400-52096800	Enhancers	Fetal Brain Male	brain
36	chr19:52096400-52096800	Enhancers	Fetal Intestine Large	intestine
37	chr19:52096400-52096800	Enhancers	Fetal Stomach	stomach
38	chr19:52096400-52096800	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr19:52096400-52096800	Enhancers	Thymus	Thymus
40	chr19:52096400-52097000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:52096400-52097000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr19:52096400-52097000	Enhancers	Esophagus	oesophagus
43	chr19:52096400-52097000	Enhancers	Placenta Amnion	Placenta Amnion
44	chr19:52096400-52097000	Enhancers	Psoas Muscle	Psoas
45	chr19:52096400-52097000	Enhancers	Right Atrium	heart
46	chr19:52096400-52097000	Enhancers	Stomach Mucosa	stomach
47	chr19:52096400-52097200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr19:52096400-52097200	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr19:52096400-52097200	Flanking Active TSS	Brain Anterior Caudate	brain
50	chr19:52096400-52097200	Flanking Active TSS	Brain Cingulate Gyrus	brain

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