Variant report

Variant	rs28673156
Chromosome Location	chr9:98247790-98247791
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98239360..98245560-chr9:98246637..98251770,7	MCF-7	breast:
2	chr9:98189018..98191444-chr9:98246516..98248115,2	MCF-7	breast:
3	chr9:98247307..98248885-chr9:98260285..98262282,2	MCF-7	breast:
4	chr9:98246647..98248663-chr9:98399249..98402157,2	K562	blood:
5	chr9:98243853..98250190-chr9:98264163..98273969,14	MCF-7	breast:
6	chr9:98246124..98248586-chr9:98264978..98268110,3	K562	blood:

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

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10512249	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909892	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs16909898	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909902	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909904	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909922	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1805155	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2036963	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282041	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2282043	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28372566	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28377268	0.86[EUR][1000 genomes]
rs28390100	0.84[AFR][1000 genomes]
rs28418339	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427480	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28429270	0.92[AFR][1000 genomes]
rs28446116	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28446321	0.95[EUR][1000 genomes]
rs28448271	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28457693	0.87[EUR][1000 genomes]
rs28474857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493225	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28494679	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs28510415	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28520225	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28535536	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs28583690	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28601668	0.92[AFR][1000 genomes]
rs28676757	0.92[AFR][1000 genomes]
rs28698995	0.80[AFR][1000 genomes]
rs28706464	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28711421	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780573	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3824488	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149656	0.88[EUR][1000 genomes]
rs59015093	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59925771	0.96[EUR][1000 genomes]
rs60150206	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60417486	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs867452	0.81[AFR][1000 genomes];0.88[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
rs28673156	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98223400-98266400	Weak transcription	Hela-S3	cervix
2	chr9:98226000-98248400	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	chr9:98232200-98261200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr9:98239400-98251400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr9:98239600-98253800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr9:98239800-98260000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr9:98240200-98267400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:98240400-98256200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr9:98240800-98259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:98241000-98258400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr9:98241200-98248800	Weak transcription	Colonic Mucosa	Colon
17	chr9:98242000-98251200	Weak transcription	K562	blood
18	chr9:98242000-98256400	Weak transcription	Esophagus	oesophagus
19	chr9:98242200-98256200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr9:98242400-98253400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr9:98242400-98253600	Weak transcription	Spleen	Spleen
22	chr9:98242400-98256200	Weak transcription	NHLF	lung
23	chr9:98242400-98266400	Weak transcription	HSMMtube	muscle
24	chr9:98242600-98247800	Weak transcription	Liver	Liver
25	chr9:98242600-98256200	Weak transcription	Placenta	Placenta
26	chr9:98242800-98253800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr9:98242800-98256600	Weak transcription	Fetal Kidney	kidney
28	chr9:98242800-98266600	Weak transcription	Adipose Nuclei	Adipose
29	chr9:98243000-98248800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:98243000-98253800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr9:98243000-98253800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr9:98243000-98255800	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr9:98243000-98256200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:98243000-98256800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr9:98243000-98267800	Weak transcription	Aorta	Aorta
36	chr9:98243200-98249000	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr9:98243400-98253600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr9:98243400-98256400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr9:98243600-98253400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr9:98243600-98256400	Weak transcription	HepG2	liver
41	chr9:98243800-98249800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr9:98243800-98260000	Weak transcription	HSMM	muscle
43	chr9:98244000-98255600	Weak transcription	GM12878-XiMat	blood
44	chr9:98244400-98248600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:98244400-98251000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr9:98244400-98256600	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr9:98244800-98251400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:98244800-98257000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:98245000-98248400	Strong transcription	Fetal Intestine Small	intestine
50	chr9:98245000-98256800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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