Variant report

Variant	rs1885108
Chromosome Location	chr14:24975509-24975510
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs11158727	0.82[EUR][1000 genomes]
rs11627321	0.80[EUR][1000 genomes]
rs11627992	0.82[EUR][1000 genomes]
rs11851739	0.81[EUR][1000 genomes]
rs12436014	0.81[EUR][1000 genomes]
rs12436015	0.81[EUR][1000 genomes]
rs12436183	0.81[EUR][1000 genomes]
rs12436184	0.81[EUR][1000 genomes]
rs12436713	0.82[EUR][1000 genomes]
rs12882754	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17184822	0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs1951133	1.00[ASW][hapmap];0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1951138	0.82[EUR][1000 genomes]
rs1951139	0.82[EUR][1000 genomes]
rs1951140	0.82[EUR][1000 genomes]
rs2253220	0.81[EUR][1000 genomes]
rs2273627	0.82[EUR][1000 genomes]
rs2332336	0.81[EUR][1000 genomes]
rs2332337	0.81[EUR][1000 genomes]
rs2332338	0.81[EUR][1000 genomes]
rs2332339	0.81[EUR][1000 genomes]
rs2332340	0.81[EUR][1000 genomes]
rs2332344	0.80[EUR][1000 genomes]
rs2332345	0.80[EUR][1000 genomes]
rs2332346	0.80[EUR][1000 genomes]
rs2332349	0.82[EUR][1000 genomes]
rs2332350	0.82[EUR][1000 genomes]
rs2332351	0.82[EUR][1000 genomes]
rs2877646	0.80[EUR][1000 genomes]
rs2877648	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34207026	0.80[EUR][1000 genomes]
rs35396435	0.80[EUR][1000 genomes]
rs35741729	0.80[EUR][1000 genomes]
rs4403961	0.81[EUR][1000 genomes]
rs4457901	0.82[EUR][1000 genomes]
rs4467000	0.94[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4508338	0.82[EUR][1000 genomes]
rs4547263	0.84[AFR][1000 genomes]
rs4981528	0.81[EUR][1000 genomes]
rs4982933	0.83[EUR][1000 genomes]
rs4982936	0.82[EUR][1000 genomes]
rs4982938	0.82[EUR][1000 genomes]
rs4982939	0.82[EUR][1000 genomes]
rs4982940	0.82[EUR][1000 genomes]
rs4982941	0.82[EUR][1000 genomes]
rs4982942	0.82[EUR][1000 genomes]
rs4982943	0.82[EUR][1000 genomes]
rs4982944	0.82[EUR][1000 genomes]
rs5244	0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs61999094	0.80[EUR][1000 genomes]
rs61999100	0.80[EUR][1000 genomes]
rs6573825	0.82[EUR][1000 genomes]
rs6573826	0.82[EUR][1000 genomes]
rs6573827	0.82[EUR][1000 genomes]
rs7143604	0.81[EUR][1000 genomes]
rs7152372	0.94[CEU][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7152749	0.82[EUR][1000 genomes]
rs7159031	0.81[EUR][1000 genomes]
rs7160659	0.81[EUR][1000 genomes]
rs731768	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs743215	0.82[EUR][1000 genomes]
rs753068	0.82[EUR][1000 genomes]
rs753069	0.82[EUR][1000 genomes]
rs761991	0.82[EUR][1000 genomes]
rs761993	0.82[EUR][1000 genomes]
rs761994	0.82[EUR][1000 genomes]
rs761995	0.82[EUR][1000 genomes]
rs761996	0.82[EUR][1000 genomes]
rs8005263	0.82[EUR][1000 genomes]
rs8007187	0.82[EUR][1000 genomes]
rs8011574	0.82[EUR][1000 genomes]
rs8014283	0.81[EUR][1000 genomes]
rs8015027	0.82[EUR][1000 genomes]
rs8015201	0.81[EUR][1000 genomes]
rs8015404	0.82[EUR][1000 genomes]
rs8015553	0.82[EUR][1000 genomes]
rs8017348	0.82[EUR][1000 genomes]
rs8019282	0.80[EUR][1000 genomes]
rs874397	0.82[EUR][1000 genomes]
rs911373	0.82[EUR][1000 genomes]
rs911374	0.82[EUR][1000 genomes]
rs911375	0.82[EUR][1000 genomes]
rs911376	0.82[EUR][1000 genomes]
rs911377	0.82[EUR][1000 genomes]
rs911378	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1053330	chr14:24908047-24993666	Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	n/a
4	esv2761824	chr14:24914008-24993666	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
5	nsv1043355	chr14:24914008-24993666	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
6	nsv1045732	chr14:24914008-25019317	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
7	nsv521915	chr14:24915383-24992619	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
8	nsv564062	chr14:24915383-24992619	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
9	nsv1039955	chr14:24927313-24993666	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
10	nsv1035903	chr14:24929447-24981097	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
11	nsv542001	chr14:24929447-24981097	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
12	nsv1042290	chr14:24930993-24990765	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
13	nsv542002	chr14:24930993-24990765	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
14	nsv983932	chr14:24967593-24993536	ZNF genes & repeats Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1885108	EDDM3A	cis	cerebellum	SCAN
rs1885108	RNASE8	cis	parietal	SCAN
rs1885108	PIGR	trans	cerebellum	SCAN
rs1885108	SDR39U1	cis	cerebellum	SCAN
rs1885108	RNASE10	cis	parietal	SCAN
rs1885108	CBLN3	cis	cerebellum	SCAN
rs1885108	TOX4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24971200-24977800	Weak transcription	Gastric	stomach

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