Variant report

Variant	rs890599
Chromosome Location	chr8:53334176-53334177
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1036715	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs10958319	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10958322	0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs11774725	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11779921	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11785415	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12156389	0.95[CHB][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13249499	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13270666	0.98[ASN][1000 genomes]
rs13271008	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13274219	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1371956	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1371957	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1440794	0.95[CHB][hapmap];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17228239	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2042807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2884960	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2884961	0.85[ASN][1000 genomes]
rs34006528	0.93[ASN][1000 genomes]
rs34129898	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3906806	0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs4144345	0.95[CHB][hapmap];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4873211	0.93[ASN][1000 genomes]
rs4873642	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4873643	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4873644	0.95[CHB][hapmap]
rs4873645	0.95[CHB][hapmap]
rs60679649	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6989658	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7008270	0.83[ASN][1000 genomes]
rs7016428	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9643803	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817380	chr8:53207304-54016570	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1032281	chr8:53241539-53383025	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv831317	chr8:53245921-53413275	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv890900	chr8:53265220-53491159	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv890901	chr8:53265220-53528204	Bivalent/Poised TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2761192	chr8:53278309-53613251	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv917043	chr8:53299833-53856743	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv917309	chr8:53299908-53898571	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv1016949	chr8:53300989-53530814	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1026748	chr8:53300989-53917456	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv1034284	chr8:53302090-53919610	Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv429915	chr8:53318647-53603847	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
13	nsv1019365	chr8:53320911-53560068	Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
14	nsv539610	chr8:53320911-53560068	Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
15	nsv1019641	chr8:53320911-53917456	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
16	nsv539611	chr8:53320911-53917456	Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
17	nsv890902	chr8:53330582-53949560	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
18	nsv1032726	chr8:53332059-53766425	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
19	nsv539612	chr8:53332059-53766425	Bivalent Enhancer Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
20	nsv1017736	chr8:53332059-53856829	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
21	nsv539613	chr8:53332059-53856829	Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs890599	EFCAB1	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:53324200-53339400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr8:53327400-53335400	Weak transcription	Brain Angular Gyrus	brain
3	chr8:53330200-53335000	Weak transcription	Brain Hippocampus Middle	brain
4	chr8:53330200-53335400	Weak transcription	Brain Substantia Nigra	brain
5	chr8:53331000-53335200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr8:53331000-53336200	Weak transcription	Brain Germinal Matrix	brain
7	chr8:53332400-53335800	Weak transcription	Fetal Brain Male	brain
8	chr8:53333600-53335400	Weak transcription	Brain Anterior Caudate	brain
9	chr8:53333800-53334400	Enhancers	Brain Cingulate Gyrus	brain

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