Variant report

Variant	rs28520225
Chromosome Location	chr9:98243187-98243188
allele	A/C
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	RUNX3	chr9:98243156-98243787	GM12878	blood:	n/a	n/a
2	PAX5	chr9:98243179-98243692	GM12878	blood:	n/a	n/a
3	MAFK	chr9:98242973-98243259	HepG2	liver:	n/a	chr9:98243120-98243134

No.	Distal block	Cell Line	Cell type
1	chr9:98241516..98243611-chr9:98244641..98247119,2	K562	blood:
2	chr9:98243031..98244911-chr9:98259333..98262016,2	K562	blood:
3	chr9:98239525..98243679-chr9:98243925..98247581,3	K562	blood:

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

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10512249	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16909892	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16909898	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs16909902	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs16909904	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16909922	0.83[EUR][1000 genomes]
rs1805155	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2036963	0.87[EUR][1000 genomes]
rs2282040	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2282041	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282043	0.87[EUR][1000 genomes]
rs28372566	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28418339	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28427480	0.83[EUR][1000 genomes]
rs28446116	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28446321	0.83[EUR][1000 genomes]
rs28448271	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28474857	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28493225	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28494679	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28510415	0.88[EUR][1000 genomes]
rs28535421	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28535536	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28583690	0.87[EUR][1000 genomes]
rs28673156	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28706464	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28711421	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28733891	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3780573	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3824488	0.88[EUR][1000 genomes]
rs56149656	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59015093	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59925771	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60150206	0.82[EUR][1000 genomes]
rs60417486	0.82[EUR][1000 genomes]
rs867452	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28520225	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 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	chr9:98225800-98244000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:98226000-98248400	Weak transcription	HUVEC	blood vessel
4	chr9:98226000-98251000	Weak transcription	Osteobl	bone
5	chr9:98226200-98243400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr9:98226200-98254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:98226400-98247800	Weak transcription	Stomach Mucosa	stomach
8	chr9:98226600-98253800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr9:98227000-98243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:98227000-98243600	Strong transcription	Fetal Intestine Small	intestine
11	chr9:98227200-98244800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:98227600-98248800	Weak transcription	Small Intestine	intestine
13	chr9:98227800-98243200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr9:98228000-98243400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:98229800-98246800	Weak transcription	Colon Smooth Muscle	Colon
16	chr9:98232200-98261200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:98233400-98243400	Strong transcription	Fetal Lung	lung
18	chr9:98233800-98243400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr9:98237400-98243600	Strong transcription	HepG2	liver
20	chr9:98238200-98246400	Weak transcription	Psoas Muscle	Psoas
21	chr9:98239400-98247200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr9:98239400-98251400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:98239600-98253800	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr9:98239800-98243800	Strong transcription	HSMM	muscle
25	chr9:98239800-98260000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr9:98240000-98247600	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr9:98240200-98243600	Enhancers	Brain Germinal Matrix	brain
28	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:98240400-98243800	Strong transcription	Duodenum Mucosa	Duodenum
30	chr9:98240400-98246400	Weak transcription	Right Ventricle	heart
31	chr9:98240400-98256200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:98240600-98243400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr9:98240600-98245000	Enhancers	Brain Substantia Nigra	brain
34	chr9:98240800-98243200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr9:98240800-98259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:98241000-98243400	Weak transcription	Primary T cells from cord blood	blood
37	chr9:98241000-98258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:98241200-98248800	Weak transcription	Colonic Mucosa	Colon
39	chr9:98241400-98243200	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:98241400-98243400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:98241400-98243400	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr9:98241400-98244400	Weak transcription	A549	lung
43	chr9:98241600-98243600	Strong transcription	Fetal Stomach	stomach
44	chr9:98241600-98246400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:98242000-98243600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:98242000-98245200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr9:98242000-98245800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr9:98242000-98251200	Weak transcription	K562	blood
49	chr9:98242000-98256400	Weak transcription	Esophagus	oesophagus
50	chr9:98242200-98243800	Enhancers	Brain Angular Gyrus	brain

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