Variant report

Variant	rs3780573
Chromosome Location	chr9:98239503-98239504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98238631..98241380-chr9:98256472..98259143,2	K562	blood:
2	chr9:98228127..98229820-chr9:98239088..98240889,2	K562	blood:
3	chr9:98236732..98239700-chr9:98240483..98242788,2	MCF-7	breast:
4	chr9:98238893..98240402-chr9:98242216..98244216,2	K562	blood:
5	chr9:98233432..98236653-chr9:98236835..98241063,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271314	Chromatin interaction
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10512249	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909892	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16909898	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909902	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909904	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16909922	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1805155	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2036963	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282040	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282041	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2282043	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28372566	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28377268	0.86[EUR][1000 genomes]
rs28418339	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427480	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28446116	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28446321	0.95[EUR][1000 genomes]
rs28448271	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28457693	0.87[EUR][1000 genomes]
rs28474857	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28493225	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28494679	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28510415	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28520225	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28535536	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28583690	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28673156	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28706464	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs28711421	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3824488	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56149656	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59015093	0.92[AFR][1000 genomes];0.89[AMR][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	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs867452	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3780573	PTCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 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	chr9:98225800-98239600	Weak transcription	HMEC	breast
3	chr9:98225800-98239800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:98225800-98244000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr9:98226000-98248400	Weak transcription	HUVEC	blood vessel
6	chr9:98226000-98251000	Weak transcription	Osteobl	bone
7	chr9:98226200-98240800	Strong transcription	Fetal Intestine Large	intestine
8	chr9:98226200-98243400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr9:98226200-98254000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr9:98226400-98243000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr9:98226400-98247800	Weak transcription	Stomach Mucosa	stomach
12	chr9:98226600-98239600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr9:98226600-98239600	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:98226600-98240000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr9:98226600-98240200	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr9:98226600-98253800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr9:98227000-98242600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:98227000-98242800	Strong transcription	Fetal Muscle Leg	muscle
19	chr9:98227000-98243600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:98227000-98243600	Strong transcription	Fetal Intestine Small	intestine
21	chr9:98227200-98243000	Strong transcription	Fetal Muscle Trunk	muscle
22	chr9:98227200-98243000	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:98227200-98244800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr9:98227400-98239600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:98227400-98242000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:98227400-98242800	Strong transcription	Adipose Nuclei	Adipose
27	chr9:98227600-98248800	Weak transcription	Small Intestine	intestine
28	chr9:98227800-98243200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr9:98228000-98240400	Strong transcription	Left Ventricle	heart
30	chr9:98228000-98243400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr9:98229800-98246800	Weak transcription	Colon Smooth Muscle	Colon
32	chr9:98231000-98239800	Weak transcription	HSMM	muscle
33	chr9:98231800-98240200	Weak transcription	Fetal Heart	heart
34	chr9:98231800-98240800	Weak transcription	A549	lung
35	chr9:98232200-98241200	Weak transcription	K562	blood
36	chr9:98232200-98261200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr9:98233200-98240800	Weak transcription	NHDF-Ad	bronchial
38	chr9:98233400-98242800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:98233400-98242800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr9:98233400-98243400	Strong transcription	Fetal Lung	lung
41	chr9:98233800-98239800	Strong transcription	Stomach Smooth Muscle	stomach
42	chr9:98233800-98240400	Strong transcription	Gastric	stomach
43	chr9:98233800-98240800	Strong transcription	Ovary	ovary
44	chr9:98233800-98243400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:98234000-98239600	Strong transcription	Fetal Brain Female	brain
46	chr9:98234200-98239600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:98234200-98243000	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr9:98234200-98243000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr9:98234400-98239800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr9:98234400-98242600	Strong transcription	Liver	Liver

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