Variant report

Variant	rs28372566
Chromosome Location	chr9:98244978-98244979
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	JUN	chr9:98244904-98245098	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr9:98243853..98250190-chr9:98264163..98273969,14	MCF-7	breast:
2	chr9:98239525..98243679-chr9:98243925..98247581,3	K562	blood:
3	chr9:98243813..98245520-chr9:98278073..98280369,2	K562	blood:
4	chr9:98241516..98243611-chr9:98244641..98247119,2	K562	blood:

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

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10512249	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs16909892	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16909898	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16909902	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16909904	0.92[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs16909922	0.83[EUR][1000 genomes]
rs1805155	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2036963	0.87[EUR][1000 genomes]
rs2282040	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2282041	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282043	0.87[EUR][1000 genomes]
rs28418339	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28427480	0.83[EUR][1000 genomes]
rs28446116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28446321	0.83[EUR][1000 genomes]
rs28448271	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28474857	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28493225	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28494679	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28510415	0.88[EUR][1000 genomes]
rs28520225	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28535421	0.90[ASN][1000 genomes]
rs28535536	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28583690	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28673156	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28706464	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28711421	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28733891	0.90[ASN][1000 genomes]
rs3780573	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3824488	0.88[EUR][1000 genomes]
rs56149656	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59015093	0.95[AFR][1000 genomes];0.89[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	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28372566	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

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	chr9:98226000-98248400	Weak transcription	HUVEC	blood vessel
3	chr9:98226000-98251000	Weak transcription	Osteobl	bone
4	chr9:98226200-98254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr9:98226400-98247800	Weak transcription	Stomach Mucosa	stomach
6	chr9:98226600-98253800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr9:98227600-98248800	Weak transcription	Small Intestine	intestine
8	chr9:98229800-98246800	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:98232200-98261200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:98238200-98246400	Weak transcription	Psoas Muscle	Psoas
11	chr9:98239400-98247200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:98239400-98251400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:98239600-98253800	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr9:98239800-98260000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:98240000-98247600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr9:98240400-98246400	Weak transcription	Right Ventricle	heart
18	chr9:98240400-98256200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:98240600-98245000	Enhancers	Brain Substantia Nigra	brain
20	chr9:98240800-98259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:98241000-98258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:98241200-98248800	Weak transcription	Colonic Mucosa	Colon
23	chr9:98241600-98246400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:98242000-98245200	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr9:98242000-98245800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr9:98242000-98251200	Weak transcription	K562	blood
27	chr9:98242000-98256400	Weak transcription	Esophagus	oesophagus
28	chr9:98242200-98256200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:98242400-98245800	Weak transcription	Gastric	stomach
30	chr9:98242400-98246400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr9:98242400-98246400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr9:98242400-98253400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr9:98242400-98253600	Weak transcription	Spleen	Spleen
34	chr9:98242400-98256200	Weak transcription	NHLF	lung
35	chr9:98242400-98266400	Weak transcription	HSMMtube	muscle
36	chr9:98242600-98245600	Enhancers	Fetal Brain Male	brain
37	chr9:98242600-98245800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr9:98242600-98246000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr9:98242600-98246400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr9:98242600-98247800	Weak transcription	Liver	Liver
41	chr9:98242600-98256200	Weak transcription	Placenta	Placenta
42	chr9:98242800-98245800	Weak transcription	Left Ventricle	heart
43	chr9:98242800-98245800	Weak transcription	Lung	lung
44	chr9:98242800-98246000	Weak transcription	Fetal Heart	heart
45	chr9:98242800-98246400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr9:98242800-98246400	Weak transcription	Pancreas	Pancrea
47	chr9:98242800-98246800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:98242800-98253800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr9:98242800-98256600	Weak transcription	Fetal Kidney	kidney
50	chr9:98242800-98266600	Weak transcription	Adipose Nuclei	Adipose

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