Variant report

Variant	rs1508222
Chromosome Location	chr4:175148556-175148557
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FBXO8-1	chr4:175148433-175148577	ucscGeneNc_uc003itn_1

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10520275	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs11555602	1.00[JPT][hapmap]
rs11929798	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs11933187	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs11942947	0.92[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs11944262	1.00[CHB][hapmap];0.87[MEX][hapmap]
rs11947136	0.81[EUR][1000 genomes]
rs13101580	0.89[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs13124698	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13128257	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs14278	1.00[JPT][hapmap]
rs17060409	1.00[JPT][hapmap]
rs17060445	1.00[JPT][hapmap]
rs17291087	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17291128	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17291408	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs17357120	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876515	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2332836	0.96[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34407356	0.81[EUR][1000 genomes]
rs34888351	0.89[EUR][1000 genomes]
rs35332594	0.80[EUR][1000 genomes]
rs35622584	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41279509	0.86[ASN][1000 genomes]
rs4287982	1.00[CHB][hapmap]
rs4695915	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4695919	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs4695922	0.80[CEU][hapmap]
rs6553777	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs6824643	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs6851312	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs7661236	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7669484	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7681841	1.00[JPT][hapmap]
rs7692518	1.00[JPT][hapmap]
rs7697587	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016910	chr4:174952788-175349057	Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv537363	chr4:174952788-175349057	Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv881449	chr4:174984230-175225452	Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv596234	chr4:175053051-175361437	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1508222	KIAA1712	Cis_1M	lymphoblastoid	RTeQTL
rs1508222	KIAA1712	cis	parietal	SCAN
rs1508222	KIAA1712	cis	multi-tissue	Pritchard
rs1508222	KIAA1712	cis	cerebellum	SCAN
rs1508222	CEP44	cis	Esophagus Muscularis	GTEx
rs1508222	CEP44	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:175146600-175158000	Weak transcription	Placenta	Placenta
2	chr4:175147000-175157000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr4:175147000-175157200	Weak transcription	Liver	Liver
4	chr4:175147000-175163000	Weak transcription	Fetal Stomach	stomach
5	chr4:175147600-175157000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr4:175147600-175195200	Weak transcription	Psoas Muscle	Psoas
7	chr4:175148000-175150200	Weak transcription	Colon Smooth Muscle	Colon

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