Variant report

Variant	rs12487204
Chromosome Location	chr3:59846067-59846068
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCTD6-8	chr3:59846047-59846080	NONHSAT090156

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11130739	0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11923964	0.97[ASN][1000 genomes]
rs11928015	0.97[ASN][1000 genomes]
rs13322831	0.98[ASN][1000 genomes]
rs1905863	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2220227	0.94[ASN][1000 genomes]
rs2253211	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253303	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2629875	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3112497	0.81[CHB][hapmap]
rs4679619	0.90[ASN][1000 genomes]
rs499323	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56279723	0.91[ASN][1000 genomes]
rs57341675	0.90[ASN][1000 genomes]
rs589522	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591934	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs606735	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609891	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs610766	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612759	0.89[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs612947	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs615542	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs623014	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs623032	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs632140	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs633189	0.81[CHB][hapmap]
rs639244	0.95[CHB][hapmap];0.87[CHD][hapmap];0.86[ASN][1000 genomes]
rs6446085	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs646372	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650215	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs652105	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs675743	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs675758	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs681119	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs684584	1.00[CHB][hapmap];0.92[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs7621132	0.80[CHB][hapmap]
rs7629400	1.00[ASN][1000 genomes]
rs7647491	0.80[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs780714	0.92[ASN][1000 genomes]
rs923141	0.95[ASN][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	nsv1014601	chr3:59666609-59888166	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv460564	chr3:59821071-59927727	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv590384	chr3:59821071-59927727	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv460565	chr3:59842644-59877988	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv470616	chr3:59842644-59877988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv590385	chr3:59842644-59877988	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv590386	chr3:59846067-59912377	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12487204	CADPS	cis	cerebellum	SCAN
rs12487204	C3orf67	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59834000-59848000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr3:59843600-59853200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:59843600-59853200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr3:59843600-59854200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:59843800-59846800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:59843800-59848000	Weak transcription	Dnd41	blood
7	chr3:59843800-59852800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:59844000-59848400	Weak transcription	Primary T cells from cord blood	blood
9	chr3:59844400-59848800	Weak transcription	Fetal Thymus	thymus

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