Variant report

Variant	rs683470
Chromosome Location	chr15:34273114-34273115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs2632086	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2632095	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2702310	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs28505823	1.00[EUR][1000 genomes]
rs34961127	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4041435	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs476121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs476814	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs480616	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs493857	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs494935	0.86[CHB][hapmap]
rs499366	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs499457	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs501012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs501432	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs504714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs505720	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap]
rs526971	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs527834	0.84[GIH][hapmap];0.83[LWK][hapmap]
rs529672	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs530700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535732	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs553598	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs553655	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs554293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs554417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs554542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs557225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs558160	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs558923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs561906	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs571458	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs592585	1.00[EUR][1000 genomes]
rs593007	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603479	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs606126	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs606990	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs636165	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs637055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs638021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs638169	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs661968	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs663273	0.86[CHB][hapmap]
rs676281	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.90[ASN][1000 genomes]
rs676316	0.86[CHB][hapmap]
rs683915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs686966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7176348	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs8035805	1.00[CEU][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043046	chr15:33714908-34321330	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1044844	chr15:34065524-34296829	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv456790	chr15:34264018-34281733	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv568923	chr15:34264018-34281733	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs683470	AVEN	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34236800-34277200	Weak transcription	Left Ventricle	heart
2	chr15:34238000-34282400	Weak transcription	Ovary	ovary
3	chr15:34261200-34277200	Weak transcription	Brain Anterior Caudate	brain
4	chr15:34263800-34277200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:34264400-34277000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:34264800-34281200	Weak transcription	GM12878-XiMat	blood
7	chr15:34265200-34299600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:34265400-34294200	Weak transcription	Fetal Stomach	stomach
9	chr15:34265400-34311800	Weak transcription	Liver	Liver
10	chr15:34269600-34274800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:34269800-34273400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:34269800-34273600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr15:34269800-34275600	Weak transcription	Brain Angular Gyrus	brain
14	chr15:34270000-34276800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr15:34270200-34277400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr15:34271600-34277200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:34271600-34277400	Weak transcription	Pancreas	Pancrea
18	chr15:34272400-34273800	Enhancers	Fetal Lung	lung
19	chr15:34272800-34273200	Enhancers	Brain Substantia Nigra	brain
20	chr15:34273000-34277600	Weak transcription	NHEK	skin

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