Variant report

Variant	rs41360845
Chromosome Location	chr9:2234724-2234725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:2226247..2228750-chr9:2234155..2236078,2	MCF-7	breast:

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12551293	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12554928	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17455320	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17455446	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2093831	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2093833	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2104343	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4358850	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4373573	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62528846	0.82[AMR][1000 genomes]
rs62528847	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62528850	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62536745	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62536746	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62536747	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62537909	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7466384	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7467600	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016148	chr9:1457605-2361750	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv539916	chr9:1457605-2361750	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv892057	chr9:2144687-2241994	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv892059	chr9:2198627-2255397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1033628	chr9:2215179-2303623	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv539927	chr9:2215179-2303623	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv892060	chr9:2218129-2261944	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
11	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv6457	chr9:2228493-2271756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv892061	chr9:2229694-2262889	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv1029947	chr9:2233969-2364269	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41360845	GLIS3	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2223600-2240800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr9:2230000-2234800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:2230000-2241200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:2230200-2241200	Weak transcription	Stomach Mucosa	stomach
5	chr9:2231200-2235600	Enhancers	Fetal Stomach	stomach
6	chr9:2231400-2235800	Enhancers	Fetal Heart	heart
7	chr9:2231600-2235600	Enhancers	Colon Smooth Muscle	Colon
8	chr9:2232400-2234800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:2232600-2234800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr9:2233600-2235600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr9:2233600-2235600	Enhancers	Ovary	ovary
12	chr9:2233600-2235600	Enhancers	HSMMtube	muscle
13	chr9:2233600-2235800	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr9:2233800-2235400	Enhancers	Fetal Muscle Trunk	muscle
15	chr9:2233800-2235400	Enhancers	Fetal Muscle Leg	muscle
16	chr9:2233800-2235600	Enhancers	Fetal Brain Male	brain
17	chr9:2233800-2236200	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr9:2234000-2234800	Enhancers	Brain Germinal Matrix	brain
19	chr9:2234000-2234800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:2234000-2235400	Enhancers	HSMM	muscle
21	chr9:2234200-2235000	Enhancers	HMEC	breast
22	chr9:2234200-2235200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:2234200-2235200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr9:2234200-2235200	Enhancers	NHEK	skin
25	chr9:2234200-2235600	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr9:2234200-2235600	Enhancers	Fetal Lung	lung
27	chr9:2234400-2234800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr9:2234400-2235000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:2234400-2235000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:2234400-2235000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr9:2234400-2235000	Enhancers	Brain Hippocampus Middle	brain
32	chr9:2234400-2235000	Enhancers	Colonic Mucosa	Colon
33	chr9:2234400-2235200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr9:2234400-2235200	Enhancers	Brain Anterior Caudate	brain
35	chr9:2234400-2235200	Enhancers	Fetal Brain Female	brain
36	chr9:2234400-2235200	Enhancers	Placenta	Placenta
37	chr9:2234400-2235200	Enhancers	Right Ventricle	heart
38	chr9:2234400-2235400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:2234400-2235400	Enhancers	Esophagus	oesophagus
40	chr9:2234400-2235400	Enhancers	Psoas Muscle	Psoas
41	chr9:2234400-2235600	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr9:2234400-2235600	Enhancers	Fetal Kidney	kidney
43	chr9:2234400-2235600	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr9:2234400-2235600	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr9:2234400-2236000	Enhancers	Left Ventricle	heart
46	chr9:2234600-2234800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr9:2234600-2234800	Enhancers	Stomach Smooth Muscle	stomach
48	chr9:2234600-2235000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:2234600-2235000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:2234600-2235400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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