Variant report

Variant	rs60417486
Chromosome Location	chr9:98262178-98262179
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:98077549..98081770-chr9:98260761..98263260,3	MCF-7	breast:
2	chr9:98247307..98248885-chr9:98260285..98262282,2	MCF-7	breast:
3	chr9:98187019..98190552-chr9:98258756..98262395,5	MCF-7	breast:
4	chr9:98261417..98264468-chr9:98264904..98267634,4	MCF-7	breast:
5	chr9:98255984..98258555-chr9:98260350..98263528,4	K562	blood:
6	chr9:98248481..98249380-chr9:98261714..98262530,2	MCF-7	breast:
7	chr9:98254931..98258273-chr9:98260384..98262387,3	MCF-7	breast:
8	chr9:98262143..98268122-chr9:98269863..98275996,9	MCF-7	breast:
9	chr9:98253775..98259048-chr9:98260307..98264013,8	K562	blood:
10	chr9:98262094..98265423-chr9:98266222..98270404,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000237857	Chromatin interaction
ENSG00000271155	Chromatin interaction
ENSG00000185920	Chromatin interaction
ENSG00000158169	Chromatin interaction
ENSG00000271314	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10512247	0.85[ASN][1000 genomes]
rs10512249	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16909892	0.82[EUR][1000 genomes]
rs16909898	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16909902	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16909904	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16909922	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909978	0.82[ASN][1000 genomes]
rs1805155	0.82[EUR][1000 genomes]
rs2036963	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282040	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282041	0.82[EUR][1000 genomes]
rs2282043	0.95[EUR][1000 genomes]
rs28372566	0.82[EUR][1000 genomes]
rs28377268	0.80[EUR][1000 genomes]
rs28418339	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28427480	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28446116	0.82[EUR][1000 genomes]
rs28446321	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28448271	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28457693	0.81[EUR][1000 genomes]
rs28474857	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28493225	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28494679	0.82[EUR][1000 genomes]
rs28510415	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28520225	0.82[EUR][1000 genomes]
rs28535536	0.82[EUR][1000 genomes]
rs28583690	0.95[EUR][1000 genomes]
rs28673156	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28706464	0.83[EUR][1000 genomes]
rs28711421	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3780573	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3824488	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56149656	0.82[EUR][1000 genomes]
rs59015093	0.82[EUR][1000 genomes]
rs59925771	0.89[EUR][1000 genomes]
rs60150206	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867452	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60417486	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
2	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:98242400-98266400	Weak transcription	HSMMtube	muscle
4	chr9:98242800-98266600	Weak transcription	Adipose Nuclei	Adipose
5	chr9:98243000-98267800	Weak transcription	Aorta	Aorta
6	chr9:98249200-98263600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr9:98250400-98262800	Weak transcription	Stomach Mucosa	stomach
8	chr9:98253400-98262400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr9:98254000-98267400	Weak transcription	Small Intestine	intestine
10	chr9:98255600-98265000	Genic enhancers	Fetal Stomach	stomach
11	chr9:98257000-98262200	Weak transcription	HepG2	liver
12	chr9:98257000-98262800	Enhancers	Brain Substantia Nigra	brain
13	chr9:98257000-98264200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr9:98257000-98264200	Weak transcription	Gastric	stomach
15	chr9:98257400-98262200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr9:98257400-98264400	Genic enhancers	Fetal Lung	lung
17	chr9:98257400-98266600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:98257400-98267000	Enhancers	Brain Hippocampus Middle	brain
19	chr9:98257600-98262200	Weak transcription	Fetal Heart	heart
20	chr9:98257600-98262200	Weak transcription	Pancreas	Pancrea
21	chr9:98258000-98264200	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr9:98258000-98266400	Enhancers	Ovary	ovary
23	chr9:98258600-98262200	Weak transcription	GM12878-XiMat	blood
24	chr9:98258600-98262600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr9:98258600-98266400	Weak transcription	Esophagus	oesophagus
26	chr9:98259200-98262400	Enhancers	Osteobl	bone
27	chr9:98259600-98262400	Strong transcription	Fetal Intestine Small	intestine
28	chr9:98259600-98263000	Enhancers	Placenta	Placenta
29	chr9:98259600-98263000	Enhancers	Lung	lung
30	chr9:98259600-98263000	Enhancers	NHLF	lung
31	chr9:98259600-98266600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:98259800-98263000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:98259800-98263000	Enhancers	Brain Anterior Caudate	brain
34	chr9:98260000-98262200	Weak transcription	Fetal Kidney	kidney
35	chr9:98260000-98262200	Weak transcription	Right Atrium	heart
36	chr9:98260000-98262600	Enhancers	NH-A	brain
37	chr9:98260000-98262800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr9:98260000-98264200	Weak transcription	Psoas Muscle	Psoas
39	chr9:98260000-98266400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr9:98260000-98266600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr9:98260200-98264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr9:98260200-98264600	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:98260200-98264800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr9:98260400-98262200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr9:98260400-98262200	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr9:98260400-98262600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr9:98260400-98263400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr9:98260400-98264200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr9:98260400-98265200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr9:98260400-98265400	Weak transcription	A549	lung

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