Variant report

Variant	rs28504650
Chromosome Location	chr9:98257842-98257843
allele	C/T
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	MXI1	chr9:98255701-98258478	SK-N-SH	brain:	n/a	chr9:98256240-98256255 chr9:98256344-98256353

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98079431..98081822-chr9:98257356..98260228,2	K562	blood:

Variant related genes	Relation type
PTCH1	TF binding region
ENSG00000158169	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10512248	0.91[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1355619	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1355620	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16909919	0.91[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2066829	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2236406	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2236407	0.92[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2274692	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2282042	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2297086	0.92[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2297088	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28457763	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]
rs28495472	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28496034	0.88[ASN][1000 genomes]
rs28536201	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28557305	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28620532	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28620668	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28629854	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]
rs28701981	0.87[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3758302	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4448343	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	nsv1053434	chr9:98248328-98259178	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

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	chr9:98239800-98260000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:98240800-98259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:98241000-98258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:98242400-98266400	Weak transcription	HSMMtube	muscle
8	chr9:98242800-98266600	Weak transcription	Adipose Nuclei	Adipose
9	chr9:98243000-98267800	Weak transcription	Aorta	Aorta
10	chr9:98243800-98260000	Weak transcription	HSMM	muscle
11	chr9:98246600-98259600	Weak transcription	Right Atrium	heart
12	chr9:98248000-98258400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:98249200-98263600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:98250400-98262800	Weak transcription	Stomach Mucosa	stomach
15	chr9:98253400-98261000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr9:98253400-98262400	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr9:98254000-98267400	Weak transcription	Small Intestine	intestine
18	chr9:98255600-98265000	Genic enhancers	Fetal Stomach	stomach
19	chr9:98255800-98260200	Enhancers	Fetal Brain Male	brain
20	chr9:98256600-98258400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:98256600-98259000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr9:98256600-98259000	Enhancers	H9 Cell Line	embryonic stem cell
23	chr9:98256600-98260400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr9:98256600-98261200	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr9:98256600-98261800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr9:98256800-98258000	Enhancers	Brain Angular Gyrus	brain
27	chr9:98256800-98258000	Enhancers	Spleen	Spleen
28	chr9:98256800-98258400	Enhancers	Brain Cingulate Gyrus	brain
29	chr9:98256800-98258600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
30	chr9:98256800-98260200	Enhancers	iPS-18 Cell Line	embryonic stem cell
31	chr9:98257000-98258000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:98257000-98258000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr9:98257000-98258000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
34	chr9:98257000-98258400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr9:98257000-98259600	Weak transcription	Left Ventricle	heart
36	chr9:98257000-98260400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr9:98257000-98261400	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr9:98257000-98262200	Weak transcription	HepG2	liver
39	chr9:98257000-98262800	Enhancers	Brain Substantia Nigra	brain
40	chr9:98257000-98264200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr9:98257000-98264200	Weak transcription	Gastric	stomach
42	chr9:98257200-98258000	Enhancers	Thymus	Thymus
43	chr9:98257200-98258600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:98257200-98258600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
45	chr9:98257200-98258800	Bivalent Enhancer	Fetal Thymus	thymus
46	chr9:98257200-98260400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:98257400-98258000	Enhancers	Brain Germinal Matrix	brain
48	chr9:98257400-98258000	Weak transcription	Ovary	ovary
49	chr9:98257400-98258000	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr9:98257400-98258200	Enhancers	Brain Anterior Caudate	brain

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