Variant report

Variant	rs59925771
Chromosome Location	chr9:98210941-98210942
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98202143..98207025-chr9:98207845..98211987,5	K562	blood:
2	chr9:98141744..98142409-chr9:98210461..98211518,3	MCF-7	breast:
3	chr9:98210232..98214386-chr9:98264282..98269915,4	K562	blood:
4	chr9:98210481..98212145-chr9:98266993..98269582,2	K562	blood:
5	chr9:98187259..98193172-chr9:98208629..98217669,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237857	Chromatin interaction
ENSG00000185920	Chromatin interaction
ENSG00000271155	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	0.95[EUR][1000 genomes]
rs16909892	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16909898	0.96[EUR][1000 genomes]
rs16909902	0.96[EUR][1000 genomes]
rs16909904	0.96[EUR][1000 genomes]
rs16909922	0.91[EUR][1000 genomes]
rs1805155	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2036963	0.95[EUR][1000 genomes]
rs2282040	0.96[EUR][1000 genomes]
rs2282041	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2282043	0.95[EUR][1000 genomes]
rs28372566	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28377268	0.82[EUR][1000 genomes]
rs28418339	0.95[EUR][1000 genomes]
rs28427480	0.91[EUR][1000 genomes]
rs28446116	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28446321	0.91[EUR][1000 genomes]
rs28448271	0.96[EUR][1000 genomes]
rs28457693	0.83[EUR][1000 genomes]
rs28474857	0.96[EUR][1000 genomes]
rs28493225	0.93[EUR][1000 genomes]
rs28494679	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28510415	0.96[EUR][1000 genomes]
rs28520225	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28535536	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28583690	0.95[EUR][1000 genomes]
rs28673156	0.96[EUR][1000 genomes]
rs28706464	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28711421	0.95[EUR][1000 genomes]
rs3780573	0.96[EUR][1000 genomes]
rs3824488	0.96[EUR][1000 genomes]
rs56149656	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59015093	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60150206	0.89[EUR][1000 genomes]
rs60417486	0.89[EUR][1000 genomes]
rs867452	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59925771	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98200800-98211800	Weak transcription	Fetal Brain Male	brain
2	chr9:98202000-98224600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:98203600-98211200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr9:98204400-98220400	Strong transcription	Fetal Intestine Large	intestine
5	chr9:98204600-98212800	Strong transcription	Fetal Lung	lung
6	chr9:98204600-98214400	Weak transcription	Osteobl	bone
7	chr9:98204800-98224400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:98205200-98218000	Weak transcription	Small Intestine	intestine
9	chr9:98205600-98212600	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:98206000-98216000	Weak transcription	Primary T cells from cord blood	blood
11	chr9:98206000-98224400	Weak transcription	HUVEC	blood vessel
12	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
13	chr9:98206200-98221400	Strong transcription	Fetal Intestine Small	intestine
14	chr9:98206400-98217600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr9:98206400-98218400	Weak transcription	NHEK	skin
16	chr9:98206600-98211400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:98206600-98212400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr9:98206600-98212600	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr9:98206600-98213200	Strong transcription	Lung	lung
20	chr9:98206600-98217200	Strong transcription	Liver	Liver
21	chr9:98206600-98220200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:98206600-98220200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr9:98206600-98220400	Strong transcription	Duodenum Mucosa	Duodenum
24	chr9:98206600-98221200	Strong transcription	Brain Hippocampus Middle	brain
25	chr9:98206600-98223000	Strong transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:98206600-98224000	Strong transcription	Adipose Nuclei	Adipose
27	chr9:98206600-98224600	Strong transcription	Aorta	Aorta
28	chr9:98206600-98225200	Strong transcription	Pancreas	Pancrea
29	chr9:98206800-98212200	Strong transcription	NHLF	lung
30	chr9:98206800-98212400	Strong transcription	Esophagus	oesophagus
31	chr9:98206800-98212800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:98206800-98214600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr9:98206800-98215800	Weak transcription	Stomach Mucosa	stomach
34	chr9:98206800-98219200	Strong transcription	Gastric	stomach
35	chr9:98207000-98211800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:98207000-98211800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr9:98207000-98212000	Strong transcription	Brain Germinal Matrix	brain
38	chr9:98207000-98212200	Strong transcription	Fetal Brain Female	brain
39	chr9:98207000-98221000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr9:98207000-98221800	Strong transcription	Ovary	ovary
41	chr9:98207000-98223000	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr9:98207200-98212200	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr9:98207200-98216600	Strong transcription	HepG2	liver
44	chr9:98207200-98219400	Strong transcription	Brain Substantia Nigra	brain
45	chr9:98207200-98223200	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr9:98207200-98224400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr9:98207400-98212200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr9:98207400-98224200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr9:98207600-98224400	Strong transcription	Skeletal Muscle Male	skeletal muscle
50	chr9:98208000-98215400	Genic enhancers	Fetal Stomach	stomach

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