Variant report

Variant	rs28493225
Chromosome Location	chr9:98226307-98226308
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	MAZ	chr9:98224550-98226453	IMR90	lung:	n/a	chr9:98225514-98225524

No.	Distal block	Cell Line	Cell type
1	chr9:98222216..98224760-chr9:98225950..98227870,2	MCF-7	breast:
2	chr9:98223864..98226761-chr9:98228381..98231062,3	K562	blood:
3	chr9:98223555..98229775-chr9:98269693..98275962,10	K562	blood:
4	chr9:98218910..98222494-chr9:98224731..98227835,5	K562	blood:
5	chr9:98222977..98229750-chr9:98267050..98274823,12	K562	blood:
6	chr9:98223412..98227347-chr9:98253313..98257210,3	K562	blood:

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

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10512249	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909892	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16909898	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909902	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909904	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909922	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1805155	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2036963	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282040	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282041	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2282043	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28372566	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28377268	0.83[EUR][1000 genomes]
rs28418339	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427480	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28446116	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28446321	0.92[EUR][1000 genomes]
rs28448271	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28457693	0.84[EUR][1000 genomes]
rs28474857	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28494679	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28510415	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28520225	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28535421	0.81[AMR][1000 genomes]
rs28535536	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28583690	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28673156	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706464	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28711421	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28733891	0.81[AMR][1000 genomes]
rs3780573	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3824488	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149656	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59015093	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59925771	0.93[EUR][1000 genomes]
rs60150206	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60417486	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs867452	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv949520	chr9:98204199-98238358	Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	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
5	nsv1053762	chr9:98208542-98232120	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1047465	chr9:98217524-98228225	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28493225	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
2	chr9:98218800-98227400	Genic enhancers	Fetal Stomach	stomach
3	chr9:98221400-98226400	Genic enhancers	Fetal Intestine Small	intestine
4	chr9:98221800-98232400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
6	chr9:98223600-98227600	Weak transcription	A549	lung
7	chr9:98224000-98226400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr9:98224000-98228800	Weak transcription	Liver	Liver
9	chr9:98224200-98227200	Weak transcription	Gastric	stomach
10	chr9:98224200-98227600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:98224200-98228000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr9:98224200-98228800	Weak transcription	Right Ventricle	heart
13	chr9:98224200-98229000	Weak transcription	Esophagus	oesophagus
14	chr9:98224400-98228800	Weak transcription	HepG2	liver
15	chr9:98224600-98226400	Enhancers	H1 Cell Line	embryonic stem cell
16	chr9:98224600-98226400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:98224600-98226600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr9:98224600-98228800	Weak transcription	Aorta	Aorta
19	chr9:98224800-98226600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:98225000-98226400	Enhancers	Stomach Mucosa	stomach
21	chr9:98225000-98226600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr9:98225000-98226800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:98225000-98227200	Weak transcription	Small Intestine	intestine
24	chr9:98225000-98228200	Genic enhancers	Fetal Lung	lung
25	chr9:98225000-98228800	Weak transcription	Lung	lung
26	chr9:98225200-98226400	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr9:98225200-98229000	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr9:98225400-98226400	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:98225400-98226600	Flanking Active TSS	GM12878-XiMat	blood
30	chr9:98225600-98226400	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr9:98225600-98226400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr9:98225600-98226400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr9:98225600-98226400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr9:98225600-98226400	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr9:98225600-98226400	Enhancers	Fetal Brain Male	brain
36	chr9:98225600-98226600	Genic enhancers	HUES6 Cell Line	embryonic stem cell
37	chr9:98225600-98226600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:98225600-98226600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr9:98225600-98226600	Genic enhancers	Rectal Mucosa Donor 31	rectum
40	chr9:98225600-98226800	Enhancers	Muscle Satellite Cultured Cells	--
41	chr9:98225600-98227000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr9:98225600-98227000	Enhancers	Brain Angular Gyrus	brain
43	chr9:98225600-98227200	Weak transcription	Ovary	ovary
44	chr9:98225600-98229200	Weak transcription	Spleen	Spleen
45	chr9:98225600-98234000	Weak transcription	Right Atrium	heart
46	chr9:98225800-98226400	Enhancers	Primary T cells fromperipheralblood	blood
47	chr9:98225800-98226400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr9:98225800-98226400	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr9:98225800-98226400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr9:98225800-98226400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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