Variant report

Variant	rs28427480
Chromosome Location	chr9:98264942-98264943
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98243853..98250190-chr9:98264163..98273969,14	MCF-7	breast:
2	chr9:98170943..98172976-chr9:98263782..98265543,2	K562	blood:
3	chr9:98210232..98214386-chr9:98264282..98269915,4	K562	blood:
4	chr9:98262143..98268122-chr9:98269863..98275996,9	MCF-7	breast:
5	chr9:98262094..98265423-chr9:98266222..98270404,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271155	Chromatin interaction
ENSG00000185920	Chromatin interaction

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

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

rs_ID	r²[population]
rs10512247	0.85[ASN][1000 genomes]
rs10512249	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16909892	0.83[EUR][1000 genomes]
rs16909898	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16909902	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16909904	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16909922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909978	0.82[ASN][1000 genomes]
rs1805155	0.83[EUR][1000 genomes]
rs2036963	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282040	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2282041	0.83[EUR][1000 genomes]
rs2282043	0.93[EUR][1000 genomes]
rs28372566	0.83[EUR][1000 genomes]
rs28377268	0.81[EUR][1000 genomes]
rs28418339	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28446116	0.83[EUR][1000 genomes]
rs28446321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28448271	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28457693	0.82[EUR][1000 genomes]
rs28474857	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28493225	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28494679	0.83[EUR][1000 genomes]
rs28510415	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28520225	0.83[EUR][1000 genomes]
rs28535536	0.83[EUR][1000 genomes]
rs28583690	0.93[EUR][1000 genomes]
rs28673156	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28706464	0.84[EUR][1000 genomes]
rs28711421	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3780573	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3824488	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56149656	0.83[EUR][1000 genomes]
rs59015093	0.83[EUR][1000 genomes]
rs59925771	0.91[EUR][1000 genomes]
rs60150206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60417486	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867452	0.83[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	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	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
5	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
6	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
rs28427480	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:91 , 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	chr9:98254000-98267400	Weak transcription	Small Intestine	intestine
7	chr9:98255600-98265000	Genic enhancers	Fetal Stomach	stomach
8	chr9:98257400-98266600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:98257400-98267000	Enhancers	Brain Hippocampus Middle	brain
10	chr9:98258000-98266400	Enhancers	Ovary	ovary
11	chr9:98258600-98266400	Weak transcription	Esophagus	oesophagus
12	chr9:98259600-98266600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr9:98260000-98266400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:98260000-98266600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:98260400-98265200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr9:98260400-98265400	Weak transcription	A549	lung
17	chr9:98260400-98266400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:98260400-98266400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr9:98260400-98266400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:98260800-98266400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr9:98260800-98266400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr9:98260800-98266400	Weak transcription	NHDF-Ad	bronchial
23	chr9:98260800-98266600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:98260800-98267000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr9:98261200-98265400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr9:98261400-98266800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:98261600-98266400	Weak transcription	Colon Smooth Muscle	Colon
28	chr9:98261800-98265000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr9:98262200-98265200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:98262200-98266800	Enhancers	Fetal Heart	heart
31	chr9:98262400-98265800	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr9:98262400-98266600	Weak transcription	Osteobl	bone
33	chr9:98262600-98265600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:98262600-98265600	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr9:98262600-98266400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr9:98262600-98266400	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr9:98262600-98266400	Weak transcription	HSMM	muscle
38	chr9:98262600-98266400	Weak transcription	NH-A	brain
39	chr9:98262600-98266600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr9:98262600-98266600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr9:98262800-98266400	Weak transcription	Fetal Muscle Leg	muscle
42	chr9:98262800-98266400	Weak transcription	HMEC	breast
43	chr9:98262800-98267600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr9:98263000-98265000	Weak transcription	HepG2	liver
45	chr9:98263000-98265600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr9:98263000-98265800	Weak transcription	NHLF	lung
47	chr9:98263000-98266400	Weak transcription	Fetal Intestine Small	intestine
48	chr9:98263000-98267800	Weak transcription	Placenta	Placenta
49	chr9:98263000-98267800	Weak transcription	Lung	lung
50	chr9:98263200-98265600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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