Variant report

Variant	rs26949
Chromosome Location	chr5:59825300-59825301
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC109486.1-1	chr5:59825231-59825370	ENSG00000152931
2	lnc-AC109486.1-1	chr5:59825231-59825370	NONHSAT101637

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10939860	0.82[JPT][hapmap]
rs10939862	0.82[JPT][hapmap]
rs11741754	0.87[ASW][hapmap];0.81[CEU][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap]
rs11948543	0.83[JPT][hapmap]
rs11955398	0.81[CEU][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap]
rs12514253	0.82[JPT][hapmap]
rs12515025	0.82[JPT][hapmap]
rs12517174	0.87[ASW][hapmap];0.81[CEU][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap]
rs12517207	0.87[ASW][hapmap];0.81[CEU][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap]
rs12522801	0.80[JPT][hapmap]
rs1379114	0.82[JPT][hapmap]
rs1379115	0.82[JPT][hapmap]
rs1379116	0.92[JPT][hapmap];0.85[YRI][hapmap]
rs152324	0.88[ASN][1000 genomes]
rs153152	0.82[AFR][1000 genomes]
rs17387940	0.87[ASW][hapmap];0.81[CEU][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];1.00[YRI][hapmap]
rs1870014	0.82[JPT][hapmap]
rs2061250	0.82[JPT][hapmap]
rs2409792	0.82[JPT][hapmap]
rs248912	0.82[AFR][1000 genomes]
rs26950	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs26953	0.88[ASN][1000 genomes]
rs26954	0.90[ASN][1000 genomes]
rs286153	0.82[JPT][hapmap]
rs35382	0.95[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs35383	0.95[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs35384	0.95[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs35385	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3857236	0.82[JPT][hapmap]
rs755077	0.82[JPT][hapmap]
rs9942410	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1018614	chr5:59708223-59910308	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv881711	chr5:59724947-59890278	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv598297	chr5:59734004-59862453	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs26949	mimitin	cis	multi-tissue	Pritchard
rs26949	ERCC8	cis	multi-tissue	Pritchard
rs26949	PART1	cis	temporal cortex	BrainEAC

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59817800-59829000	Weak transcription	Aorta	Aorta
2	chr5:59823600-59825400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr5:59823800-59829200	Weak transcription	Brain Substantia Nigra	brain
4	chr5:59824000-59834200	Weak transcription	Brain Angular Gyrus	brain
5	chr5:59824800-59825400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr5:59825000-59825400	Enhancers	Rectal Smooth Muscle	rectum
7	chr5:59825000-59825400	Enhancers	Monocytes-CD14+_RO01746	blood

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