Variant report

Variant	rs2589344
Chromosome Location	chr8:35397152-35397153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1371153	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1439161	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2579880	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2579882	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2579884	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2579894	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2579895	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2589329	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2589330	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2589332	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2589345	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2589349	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2589350	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2589745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2589748	0.95[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2589756	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2589757	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2589759	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017085	chr8:34742896-35594241	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv539546	chr8:34742896-35594241	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv520421	chr8:35155517-35479468	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024397	chr8:35296922-35424277	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv533420	chr8:35358115-36227536	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv1824129	chr8:35395787-35400084	Weak transcription Enhancers Active TSS Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
7	esv1842463	chr8:35395787-35400084	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
8	esv275263	chr8:35396135-35401379	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2589344	C8orf86	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:35359800-35397200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:35391600-35401400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr8:35393000-35397200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr8:35393800-35399800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr8:35395800-35397200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr8:35396200-35397600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
7	chr8:35396200-35399200	Enhancers	iPS-20b Cell Line	embryonic stem cell
8	chr8:35396600-35404000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr8:35397000-35397400	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr8:35397000-35397400	Enhancers	H1 Cell Line	embryonic stem cell
11	chr8:35397000-35397400	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr8:35397000-35398600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr8:35397000-35403600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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