Variant report

Variant	rs8085470
Chromosome Location	chr18:29521986-29521987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr18:29521981-29523799	PBDE	blood:	n/a	n/a
2	POLR2A	chr18:29521877-29523673	K562	blood:	n/a	n/a
3	MXI1	chr18:29521941-29523997	IMR90	lung:	n/a	n/a
4	MXI1	chr18:29521947-29523875	K562	blood:	n/a	n/a
5	HCFC1	chr18:29521847-29524057	Hela-S3	cervix:	n/a	n/a
6	STAT3	chr18:29521936-29522203	GM12878	blood:	n/a	n/a
7	MXI1	chr18:29521978-29525320	SK-N-SH	brain:	n/a	n/a
8	JUN	chr18:29521820-29525062	K562	blood:	n/a	chr18:29524927-29524938 chr18:29524884-29524893 chr18:29523238-29523247 chr18:29523904-29523913 chr18:29523903-29523912 chr18:29524929-29524937
9	RCOR1	chr18:29521864-29524063	IMR90	lung:	n/a	n/a
10	MXI1	chr18:29521884-29523925	GM12878	blood:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:29517111..29520943-chr18:29521139..29523956,5	MCF-7	breast:
2	chr18:29521939..29525237-chr18:29670716..29673913,4	MCF-7	breast:
3	chr18:29518719..29521005-chr18:29521192..29525426,5	MCF-7	breast:
4	chr18:29450429..29452203-chr18:29521687..29523259,2	MCF-7	breast:
5	chr18:29521665..29524441-chr18:29544834..29547590,2	K562	blood:
6	chr18:29483369..29487458-chr18:29519948..29522209,3	K562	blood:
7	chr18:29521618..29525019-chr18:29670361..29672184,4	MCF-7	breast:
8	chr18:29521522..29523729-chr18:29672844..29674625,2	MCF-7	breast:
9	chr18:29521537..29525393-chr18:29670839..29674328,7	K562	blood:
10	chr18:29520857..29524705-chr18:29670705..29674434,7	K562	blood:
11	chr18:29494660..29496304-chr18:29519916..29522258,2	K562	blood:
12	chr18:29520544..29523172-chr18:33708356..33710539,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000263823	TF binding region
TRAPPC8	TF binding region
ENSG00000265008	Chromatin interaction
ENSG00000238982	Chromatin interaction
ENSG00000222320	Chromatin interaction
ENSG00000266105	Chromatin interaction
ENSG00000153339	Chromatin interaction
ENSG00000141424	Chromatin interaction
ENSG00000134758	Chromatin interaction
ENSG00000134759	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11872757	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11873875	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11874574	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11875279	0.83[ASN][1000 genomes]
rs11876025	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11878164	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34059722	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34176695	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34888238	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72932147	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8083827	0.83[ASN][1000 genomes]
rs8083851	0.83[ASN][1000 genomes]
rs8084138	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8088671	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099528	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9965255	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431975	chr18:29311034-29527902	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1067252	chr18:29475073-29583744	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29478600-29522000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr18:29482400-29522000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:29509600-29522000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr18:29509600-29522000	Weak transcription	Lung	lung
5	chr18:29512400-29522000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr18:29516800-29522000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:29516800-29522000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr18:29520200-29526800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr18:29521000-29522000	Flanking Active TSS	Liver	Liver
10	chr18:29521000-29522200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr18:29521000-29522600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr18:29521000-29524400	Active TSS	Psoas Muscle	Psoas
13	chr18:29521200-29522000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr18:29521200-29522200	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr18:29521200-29522200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr18:29521200-29522200	Active TSS	HepG2	liver
17	chr18:29521200-29522600	Active TSS	Brain Germinal Matrix	brain
18	chr18:29521200-29524200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr18:29521200-29524400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr18:29521200-29524400	Active TSS	GM12878-XiMat	blood
21	chr18:29521200-29524800	Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr18:29521200-29524800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr18:29521200-29525200	Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr18:29521400-29522000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr18:29521400-29522000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr18:29521400-29522000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr18:29521400-29522000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr18:29521400-29522000	Weak transcription	Esophagus	oesophagus
29	chr18:29521400-29522000	Weak transcription	Gastric	stomach
30	chr18:29521400-29522000	Weak transcription	Left Ventricle	heart
31	chr18:29521400-29522000	Weak transcription	Pancreas	Pancrea
32	chr18:29521400-29522000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
33	chr18:29521400-29522000	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr18:29521400-29522000	Enhancers	Stomach Mucosa	stomach
35	chr18:29521400-29522000	Flanking Active TSS	Hela-S3	cervix
36	chr18:29521400-29522000	Flanking Active TSS	HMEC	breast
37	chr18:29521400-29522200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr18:29521400-29522400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr18:29521400-29522400	Flanking Active TSS	Dnd41	blood
40	chr18:29521400-29522800	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr18:29521400-29523600	Active TSS	Muscle Satellite Cultured Cells	--
42	chr18:29521400-29524000	Active TSS	Ovary	ovary
43	chr18:29521400-29524000	Active TSS	NHDF-Ad	bronchial
44	chr18:29521400-29524000	Active TSS	NHLF	lung
45	chr18:29521400-29524200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr18:29521400-29524200	Active TSS	HSMM	muscle
47	chr18:29521400-29524400	Active TSS	Fetal Kidney	kidney
48	chr18:29521400-29524600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:29521400-29524600	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr18:29521400-29525000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links