Variant report

Variant	rs12489021
Chromosome Location	chr3:85021664-85021665
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11127869	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12485289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1248821	0.87[ASW][hapmap]
rs12632010	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12637056	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17022112	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17022119	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17022138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17022236	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17022250	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.97[MKK][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17022300	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17043532	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs1872554	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2172846	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2200466	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2220245	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2326121	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.97[MKK][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55916509	0.85[ASN][1000 genomes]
rs62250601	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6789062	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72029051	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7646952	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

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	esv3381298	chr3:84689266-85030314	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1002058	chr3:84757044-85389876	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1001316	chr3:84773522-85071342	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv877091	chr3:84876250-85069287	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv482371	chr3:84880813-85031486	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv471620	chr3:84880814-85031486	Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv1829788	chr3:84926769-85086403	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1010140	chr3:84997012-85034281	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1000793	chr3:85020452-85051839	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:85018000-85027600	Weak transcription	Brain Substantia Nigra	brain
2	chr3:85018200-85022600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:85018200-85029200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:85018400-85025800	Weak transcription	Brain Angular Gyrus	brain
5	chr3:85018400-85027800	Weak transcription	Brain Hippocampus Middle	brain
6	chr3:85018400-85028000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr3:85018400-85029200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:85019000-85028000	Weak transcription	Brain Anterior Caudate	brain
9	chr3:85019200-85026200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:85019600-85029200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:85019800-85029200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:85020000-85030400	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:85020000-85030600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:85020200-85022600	Weak transcription	Fetal Kidney	kidney
15	chr3:85020200-85027600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:85020200-85032200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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