Variant report

Variant	rs1865094
Chromosome Location	chr19:39976969-39976970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39976804-39977342	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:39947157-39987373	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39976831-39977255	K562	blood:	n/a	n/a
4	POLR2A	chr19:39976334-39977417	K562	blood:	n/a	n/a
5	POLR2A	chr19:39976269-39977189	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr19:39976073-39977368	K562	blood:	n/a	n/a
7	POLR2A	chr19:39976297-39977284	GM12892	blood:	n/a	n/a
8	POLR2A	chr19:39976802-39977318	GM12892	blood:	n/a	n/a
9	POLR2A	chr19:39976392-39977119	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:39976304-39976969	K562	blood:	n/a	n/a
11	POLR2A	chr19:39976886-39977150	H1-hESC	embryonic stem cell:	n/a	n/a
12	HEY1	chr19:39976493-39976975	K562	blood:	n/a	n/a
13	POLR2A	chr19:39976882-39977046	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr19:39973155-39985792	PANC-1	pancreas:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:39947815..39949510-chr19:39975198..39977049,2	MCF-7	breast:
2	chr19:39913480..39916274-chr19:39975273..39977291,2	MCF-7	breast:

No data

Variant related genes	Relation type
TIMM50	TF binding region
ENSG00000196235	Chromatin interaction
ENSG00000090924	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs11882744	0.84[GIH][hapmap]
rs1529733	0.82[GIH][hapmap]
rs4802030	0.85[GIH][hapmap]
rs4803238	0.85[GIH][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1865094	B3GNT8	cis	parietal	SCAN
rs1865094	PHLDB3	cis	parietal	SCAN
rs1865094	NKPD1	cis	parietal	SCAN
rs1865094	PRKD2	cis	cerebellum	SCAN
rs1865094	MIA	cis	cerebellum	SCAN
rs1865094	CD177	cis	parietal	SCAN
rs1865094	QPCTL	cis	cerebellum	SCAN

Chromatin state (count:125 , 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	chr19:39972800-39977000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr19:39972800-39977400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:39972800-39978800	Weak transcription	NHDF-Ad	bronchial
5	chr19:39972800-39980200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:39972800-39982200	Weak transcription	Fetal Kidney	kidney
7	chr19:39972800-39983200	Strong transcription	Fetal Brain Female	brain
8	chr19:39972800-39983600	Strong transcription	Fetal Stomach	stomach
9	chr19:39972800-39984200	Weak transcription	Stomach Mucosa	stomach
10	chr19:39972800-39988600	Weak transcription	Right Atrium	heart
11	chr19:39973000-39981600	Strong transcription	NHEK	skin
12	chr19:39973000-39982000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:39973000-39983000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr19:39973000-39983000	Strong transcription	Fetal Intestine Small	intestine
15	chr19:39973000-39983800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:39973200-39983800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:39973200-39983800	Strong transcription	Fetal Muscle Leg	muscle
18	chr19:39973400-39979600	Strong transcription	HSMM	muscle
19	chr19:39973400-39981400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr19:39973400-39981400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr19:39973400-39981400	Strong transcription	Fetal Intestine Large	intestine
22	chr19:39973400-39982400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr19:39973400-39982800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:39973400-39983000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:39973400-39983000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr19:39973400-39983000	Strong transcription	Thymus	Thymus
27	chr19:39973400-39983200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:39973400-39983200	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:39973400-39983200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:39973400-39983200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr19:39973400-39983200	Strong transcription	Primary T cells from cord blood	blood
32	chr19:39973400-39983200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:39973400-39983200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:39973400-39983400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr19:39973400-39983800	Strong transcription	Brain Germinal Matrix	brain
36	chr19:39973600-39980800	Strong transcription	K562	blood
37	chr19:39973600-39981200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr19:39973600-39981400	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr19:39973600-39981400	Strong transcription	Fetal Lung	lung
40	chr19:39973600-39981400	Strong transcription	Stomach Smooth Muscle	stomach
41	chr19:39973600-39982000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:39973600-39982800	Strong transcription	Adipose Nuclei	Adipose
43	chr19:39973600-39983000	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr19:39973600-39983000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:39973600-39983200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:39973600-39983200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr19:39973600-39983200	Strong transcription	Liver	Liver
48	chr19:39973600-39983200	Strong transcription	Fetal Muscle Trunk	muscle
49	chr19:39973600-39988400	Weak transcription	Fetal Brain Male	brain
50	chr19:39973800-39980000	Strong transcription	A549	lung

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