Variant report

Variant	rs11880201
Chromosome Location	chr19:39981786-39981787
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	POLR2A	chr19:39981734-39981974	K562	blood:	n/a	n/a
2	POLR2A	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39981636-39981917	K562	blood:	n/a	n/a
4	POLR2A	chr19:39973155-39985792	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39974324..39976296-chr19:39980616..39983158,2	MCF-7	breast:
2	chr19:39930044..39931944-chr19:39980921..39983797,2	MCF-7	breast:

Variant related genes	Relation type
TIMM50	TF binding region
ENSG00000213922	Chromatin interaction
ENSG00000105197	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16973421	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28365843	1.00[ASN][1000 genomes]
rs56999463	1.00[EUR][1000 genomes]
rs73547972	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv911691	chr19:39979966-40029386	Strong transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 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	chr19:39972200-39986400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:39972800-39982200	Weak transcription	Fetal Kidney	kidney
3	chr19:39972800-39983200	Strong transcription	Fetal Brain Female	brain
4	chr19:39972800-39983600	Strong transcription	Fetal Stomach	stomach
5	chr19:39972800-39984200	Weak transcription	Stomach Mucosa	stomach
6	chr19:39972800-39988600	Weak transcription	Right Atrium	heart
7	chr19:39973000-39982000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr19:39973000-39983000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr19:39973000-39983000	Strong transcription	Fetal Intestine Small	intestine
10	chr19:39973000-39983800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:39973200-39983800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr19:39973200-39983800	Strong transcription	Fetal Muscle Leg	muscle
13	chr19:39973400-39982400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr19:39973400-39982800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr19:39973400-39983000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr19:39973400-39983000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:39973400-39983000	Strong transcription	Thymus	Thymus
18	chr19:39973400-39983200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:39973400-39983200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr19:39973400-39983200	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr19:39973400-39983200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:39973400-39983200	Strong transcription	Primary T cells from cord blood	blood
23	chr19:39973400-39983200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr19:39973400-39983200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr19:39973400-39983400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr19:39973400-39983800	Strong transcription	Brain Germinal Matrix	brain
27	chr19:39973600-39982000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr19:39973600-39982800	Strong transcription	Adipose Nuclei	Adipose
29	chr19:39973600-39983000	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr19:39973600-39983000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:39973600-39983200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:39973600-39983200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:39973600-39983200	Strong transcription	Liver	Liver
34	chr19:39973600-39983200	Strong transcription	Fetal Muscle Trunk	muscle
35	chr19:39973600-39988400	Weak transcription	Fetal Brain Male	brain
36	chr19:39973800-39983200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr19:39973800-39983800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr19:39974000-39983000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:39974000-39983200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr19:39974000-39983400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr19:39974200-39982200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr19:39974200-39982400	Strong transcription	Left Ventricle	heart
43	chr19:39974200-39983200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr19:39974400-39983200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr19:39974800-39981800	Strong transcription	Placenta	Placenta
46	chr19:39975000-39983200	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr19:39975000-39983200	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr19:39975000-39983200	Strong transcription	Skeletal Muscle Male	skeletal muscle
49	chr19:39975200-39981800	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr19:39975400-39983000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links