Variant report

Variant	rs6861054
Chromosome Location	chr5:40892204-40892205
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10067114	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10071209	0.94[ASN][1000 genomes]
rs10472345	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13156109	0.83[YRI][hapmap]
rs1376178	0.88[CEU][hapmap];0.82[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1697938	0.89[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1910016	0.83[YRI][hapmap]
rs2122569	0.88[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2443035	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2443040	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2459465	0.88[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2459467	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2597746	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs323565	0.81[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs324063	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs324066	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs324067	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs324068	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs324072	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs364443	0.84[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs420220	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs438652	0.88[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs6887212	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs837383	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs837388	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
2	nsv881467	chr5:40869802-41008650	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2757114	chr5:40874078-41009282	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	esv2759341	chr5:40874078-41009282	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv823055	chr5:40875708-41004839	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv35077	chr5:40875843-41000671	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6861054	DAB2	cis	cerebellum	SCAN
rs6861054	C5orf34	cis	parietal	SCAN
rs6861054	OXCT1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40885200-40895400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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