Variant report

Variant	rs28457763
Chromosome Location	chr9:98260514-98260515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr9:98259887-98260567	IMR90	lung:	n/a	chr9:98260447-98260460
2	MAZ	chr9:98259976-98260614	IMR90	lung:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr9:98247307..98248885-chr9:98260285..98262282,2	MCF-7	breast:
2	chr9:98187019..98190552-chr9:98258756..98262395,5	MCF-7	breast:
3	chr9:98243031..98244911-chr9:98259333..98262016,2	K562	blood:
4	chr9:98258805..98260606-chr9:98267349..98269372,2	MCF-7	breast:
5	chr9:98255984..98258555-chr9:98260350..98263528,4	K562	blood:
6	chr9:98254931..98258273-chr9:98260384..98262387,3	MCF-7	breast:
7	chr9:98248561..98250430-chr9:98258742..98261519,2	MCF-7	breast:
8	chr9:98253775..98259048-chr9:98260307..98264013,8	K562	blood:

No data

Variant related genes	Relation type
PTCH1	TF binding region
ENSG00000271155	Chromatin interaction
ENSG00000237857	Chromatin interaction
ENSG00000271314	Chromatin interaction
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10512248	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1355619	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1355620	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909919	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066829	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2236407	0.83[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2282042	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2297086	0.83[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2297088	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28495472	0.83[ASN][1000 genomes]
rs28496034	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28504650	0.91[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28536201	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28557305	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28591501	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28620668	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28629854	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28701981	0.85[JPT][hapmap];0.85[MEX][hapmap]
rs3758302	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4448343	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv1051665	chr9:98234404-98264577	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv824994	chr9:98239963-98314431	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv824995	chr9:98243455-98326547	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv824996	chr9:98245375-98283861	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28457763	ZNF367	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
2	chr9:98232200-98261200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:98242400-98266400	Weak transcription	HSMMtube	muscle
5	chr9:98242800-98266600	Weak transcription	Adipose Nuclei	Adipose
6	chr9:98243000-98267800	Weak transcription	Aorta	Aorta
7	chr9:98249200-98263600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr9:98250400-98262800	Weak transcription	Stomach Mucosa	stomach
9	chr9:98253400-98261000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:98253400-98262400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr9:98254000-98267400	Weak transcription	Small Intestine	intestine
12	chr9:98255600-98265000	Genic enhancers	Fetal Stomach	stomach
13	chr9:98256600-98261200	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr9:98256600-98261800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:98257000-98261400	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr9:98257000-98262200	Weak transcription	HepG2	liver
17	chr9:98257000-98262800	Enhancers	Brain Substantia Nigra	brain
18	chr9:98257000-98264200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr9:98257000-98264200	Weak transcription	Gastric	stomach
20	chr9:98257400-98260600	Weak transcription	Right Ventricle	heart
21	chr9:98257400-98261200	Weak transcription	Colonic Mucosa	Colon
22	chr9:98257400-98261200	Weak transcription	Fetal Intestine Large	intestine
23	chr9:98257400-98262200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:98257400-98264400	Genic enhancers	Fetal Lung	lung
25	chr9:98257400-98266600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr9:98257400-98267000	Enhancers	Brain Hippocampus Middle	brain
27	chr9:98257600-98260600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr9:98257600-98261000	Weak transcription	K562	blood
29	chr9:98257600-98262200	Weak transcription	Fetal Heart	heart
30	chr9:98257600-98262200	Weak transcription	Pancreas	Pancrea
31	chr9:98257800-98260600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr9:98257800-98261600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr9:98258000-98262000	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr9:98258000-98264200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr9:98258000-98266400	Enhancers	Ovary	ovary
36	chr9:98258400-98260800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr9:98258600-98260600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr9:98258600-98260800	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr9:98258600-98262000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:98258600-98262200	Weak transcription	GM12878-XiMat	blood
41	chr9:98258600-98262600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr9:98258600-98266400	Weak transcription	Esophagus	oesophagus
43	chr9:98259000-98260800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:98259000-98261000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr9:98259200-98262400	Enhancers	Osteobl	bone
46	chr9:98259400-98260600	Enhancers	Fetal Brain Female	brain
47	chr9:98259400-98260800	Enhancers	H9 Cell Line	embryonic stem cell
48	chr9:98259400-98260800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr9:98259400-98261400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr9:98259400-98261400	Enhancers	Brain Cingulate Gyrus	brain

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