Variant report

Variant	rs9289134
Chromosome Location	chr3:119473719-119473720
allele	C/T
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:39)

rs_ID	r²[population]
rs10511394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10934498	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs1129708	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11926554	1.00[CEU][hapmap];0.94[CHB][hapmap];0.81[EUR][1000 genomes]
rs12488820	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs13072420	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086843	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1464599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1523127	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs1523130	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs1581451	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs2276706	0.93[CHB][hapmap]
rs2461829	0.83[ASN][1000 genomes]
rs2461830	0.84[ASN][1000 genomes]
rs28424110	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34333922	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34490729	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34787921	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34948068	0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35017263	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35246961	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35576079	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3814055	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs4687882	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4688032	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688033	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60639590	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66840889	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6770006	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7613408	0.81[CHB][hapmap]
rs7643038	0.94[CHB][hapmap];0.91[CHD][hapmap]
rs7644545	0.81[CHB][hapmap]
rs9682652	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9815093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9817024	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9821892	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9847068	0.81[CHB][hapmap]
rs9848716	0.81[CHB][hapmap]
rs9865270	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011178	chr3:119437192-119589116	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv536703	chr3:119437192-119589116	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv3426402	chr3:119472162-119475860	Strong transcription Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9289134	COX17	cis	lymphoblastoid	seeQTL
rs9289134	C3orf15	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119435400-119478200	Weak transcription	Colon Smooth Muscle	Colon
2	chr3:119450600-119474200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:119451200-119475200	Weak transcription	Fetal Brain Male	brain
4	chr3:119463200-119476000	Weak transcription	Spleen	Spleen
5	chr3:119465600-119474400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:119470000-119474400	Strong transcription	Ovary	ovary
7	chr3:119470600-119474600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
8	chr3:119471000-119479400	Weak transcription	Brain Substantia Nigra	brain
9	chr3:119471200-119474800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:119471200-119475200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:119471200-119475800	Weak transcription	Brain Angular Gyrus	brain
12	chr3:119471400-119474200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:119472200-119474400	Strong transcription	Fetal Kidney	kidney
14	chr3:119472200-119474400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
15	chr3:119472400-119473800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:119472600-119474400	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr3:119472800-119473800	Strong transcription	Brain Anterior Caudate	brain
18	chr3:119473000-119479400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:119473400-119473800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:119473400-119473800	Strong transcription	Pancreas	Pancrea
21	chr3:119473600-119473800	ZNF genes & repeats	Aorta	Aorta

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