Variant report

Variant	rs1360290
Chromosome Location	chr9:117894539-117894540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1000109	0.90[MEX][hapmap]
rs10759757	0.90[MEX][hapmap]
rs10817714	0.81[AMR][1000 genomes]
rs10817715	0.81[AMR][1000 genomes]
rs10817716	0.90[MEX][hapmap]
rs10817718	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10982550	0.81[AMR][1000 genomes]
rs10982557	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10982572	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10982576	0.81[CEU][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10982598	0.88[ASN][1000 genomes]
rs1111784	0.90[MEX][hapmap]
rs11788578	0.85[CEU][hapmap]
rs11793679	0.90[MEX][hapmap]
rs11794627	0.86[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12376870	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12380363	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1335350	1.00[CHB][hapmap]
rs1414146	1.00[CHB][hapmap];0.87[GIH][hapmap]
rs16936516	0.89[MEX][hapmap]
rs2001693	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2012566	0.90[MEX][hapmap]
rs2012775	0.90[MEX][hapmap]
rs4448357	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4587405	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4979499	0.93[CEU][hapmap]
rs4979506	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57814325	0.92[ASN][1000 genomes]
rs7025283	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7029482	0.88[ASN][1000 genomes]
rs7029844	0.86[CEU][hapmap];0.92[ASN][1000 genomes]
rs7040243	1.00[CHB][hapmap];0.93[GIH][hapmap]
rs7849460	0.90[MEX][hapmap]
rs7849467	0.85[MEX][hapmap]
rs7850000	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7851185	1.00[CHB][hapmap]
rs7865971	0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats 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
2	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv893768	chr9:117853103-117903975	Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv831697	chr9:117860416-118023927	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv6681	chr9:117893926-117938609	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1360290	C9orf80	cis	cerebellum	SCAN
rs1360290	GIT1	trans	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117889400-117895000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr9:117889800-117894800	Weak transcription	Fetal Muscle Leg	muscle
3	chr9:117889800-117895200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:117890200-117894800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:117890200-117909000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr9:117890400-117895000	Weak transcription	HSMMtube	muscle
7	chr9:117890400-117895800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:117893600-117894800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:117894000-117895600	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:117894200-117894800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr9:117894200-117894800	Weak transcription	NHDF-Ad	bronchial
12	chr9:117894200-117894800	Enhancers	Osteobl	bone
13	chr9:117894200-117895000	Enhancers	NHLF	lung
14	chr9:117894200-117895400	Enhancers	Fetal Kidney	kidney
15	chr9:117894200-117898800	Enhancers	Fetal Stomach	stomach
16	chr9:117894400-117894600	Enhancers	Rectal Smooth Muscle	rectum
17	chr9:117894400-117895000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:117894400-117895000	Enhancers	HSMM	muscle
19	chr9:117894400-117895400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:117894400-117896600	Enhancers	NH-A	brain

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