Variant report

Variant	rs2145926
Chromosome Location	chr9:27193311-27193312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1360772	0.81[JPT][hapmap]
rs1360773	0.81[JPT][hapmap]
rs2252883	0.91[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs4242670	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs481294	0.91[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap]
rs491892	0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs510101	0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs511586	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs549099	0.86[JPT][hapmap]
rs558897	0.81[JPT][hapmap]
rs560551	0.81[JPT][hapmap]
rs573722	0.86[JPT][hapmap]
rs573787	0.82[ASN][1000 genomes]
rs606342	0.82[JPT][hapmap]
rs622477	0.84[ASN][1000 genomes]
rs638203	0.81[JPT][hapmap]
rs639225	0.81[JPT][hapmap]
rs654494	0.81[JPT][hapmap]
rs655392	0.81[JPT][hapmap]
rs655880	0.91[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs669102	0.88[CEU][hapmap];0.82[CHB][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs669545	0.88[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs671353	0.81[JPT][hapmap]
rs686256	0.91[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs692946	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016733	chr9:27073650-27264576	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1022313	chr9:27083369-27250505	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1017802	chr9:27088160-27262682	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1019104	chr9:27088160-27358206	Enhancers Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv6512	chr9:27155677-27200455	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv892864	chr9:27176554-27296705	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv466335	chr9:27179244-27234029	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv613946	chr9:27179244-27234029	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1009235	chr9:27189804-27196618	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2145926	TUSC1	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:27151000-27229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:27165400-27198200	Weak transcription	Ovary	ovary
3	chr9:27165400-27219200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:27166200-27205800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:27166200-27229000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr9:27178400-27197200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr9:27180800-27230600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr9:27182600-27194000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr9:27184000-27197800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:27184200-27193800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr9:27184200-27194000	Weak transcription	Psoas Muscle	Psoas
12	chr9:27184200-27212600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:27191800-27193600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:27192000-27196800	Enhancers	HUVEC	blood vessel
15	chr9:27192200-27193400	Enhancers	Adipose Nuclei	Adipose
16	chr9:27192200-27194200	Weak transcription	Osteobl	bone
17	chr9:27192400-27193600	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr9:27192400-27193800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr9:27192400-27194600	Weak transcription	NHLF	lung
20	chr9:27192600-27193800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr9:27192800-27193400	Weak transcription	Colon Smooth Muscle	Colon
22	chr9:27192800-27193400	Enhancers	Left Ventricle	heart
23	chr9:27192800-27194800	Weak transcription	Right Atrium	heart
24	chr9:27193000-27194000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr9:27193000-27194000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:27193000-27194000	Weak transcription	HSMM	muscle
27	chr9:27193000-27194200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr9:27193000-27194200	Weak transcription	HSMMtube	muscle
29	chr9:27193000-27195000	Weak transcription	Placenta	Placenta
30	chr9:27193000-27203000	Weak transcription	Aorta	Aorta
31	chr9:27193000-27204800	Weak transcription	Lung	lung
32	chr9:27193000-27209000	Weak transcription	Fetal Stomach	stomach
33	chr9:27193000-27212600	Weak transcription	Spleen	Spleen
34	chr9:27193000-27220000	Weak transcription	Fetal Muscle Leg	muscle
35	chr9:27193200-27194200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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