Variant report

Variant	rs17768235
Chromosome Location	chr9:22683792-22683793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12551699	0.90[ASN][1000 genomes]
rs13286221	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13287713	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13289091	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1375290	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1448788	0.86[ASW][hapmap]
rs1448789	0.86[ASW][hapmap]
rs2044673	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2210865	0.90[ASN][1000 genomes]
rs2383242	0.83[MEX][hapmap]
rs36034752	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62572491	0.85[AMR][1000 genomes]
rs729453	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs976732	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv869121	chr9:22382290-23232146	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2761508	chr9:22400968-22819938	Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv533941	chr9:22416549-23232146	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv892759	chr9:22502851-22705094	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv892760	chr9:22562121-22765106	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	esv3427254	chr9:22597780-22693940	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv466299	chr9:22610366-22749670	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv613786	chr9:22610366-22749670	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv892761	chr9:22625342-22690588	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv34240	chr9:22628700-22695593	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv2757327	chr9:22628931-22696345	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
14	esv2759681	chr9:22628931-22696345	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv430007	chr9:22636541-22757714	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv892763	chr9:22641633-22765106	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	nsv1030670	chr9:22669166-22697535	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
18	nsv892764	chr9:22680915-22755025	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17768235	FAM154A	cis	parietal	SCAN
rs17768235	RP11-399D6.2	cis	Artery Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22679000-22687800	Weak transcription	Pancreas	Pancrea
2	chr9:22681000-22684800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr9:22682200-22683800	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr9:22682200-22684800	Enhancers	Hela-S3	cervix
5	chr9:22682600-22683800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr9:22682600-22684000	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr9:22682600-22684200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:22682600-22684200	Enhancers	HMEC	breast
9	chr9:22682600-22684400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr9:22682600-22684400	Enhancers	NH-A	brain
11	chr9:22682800-22684000	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr9:22682800-22684000	Enhancers	Osteobl	bone
13	chr9:22682800-22684200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:22682800-22685200	Strong transcription	Liver	Liver
15	chr9:22683000-22684800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr9:22683200-22684000	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr9:22683200-22684800	Enhancers	Skeletal Muscle Male	skeletal muscle
18	chr9:22683400-22683800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:22683400-22683800	Active TSS	NHDF-Ad	bronchial
20	chr9:22683400-22684200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:22683400-22684400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr9:22683600-22684000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:22683600-22684200	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr9:22683600-22685000	Enhancers	NHLF	lung

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