Variant report

Variant	rs12535978
Chromosome Location	chr7:56723098-56723099
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10235121	1.00[CHD][hapmap]
rs10242086	1.00[CHD][hapmap]
rs10256440	1.00[CHD][hapmap]
rs10259576	1.00[CHD][hapmap]
rs1105305	1.00[CHD][hapmap]
rs11970784	0.82[EUR][1000 genomes]
rs11976165	0.82[CEU][hapmap];0.90[TSI][hapmap]
rs11978242	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs11981923	0.83[EUR][1000 genomes]
rs11982672	0.83[EUR][1000 genomes]
rs11982992	0.82[EUR][1000 genomes]
rs11984288	0.83[EUR][1000 genomes]
rs12532086	1.00[ASN][1000 genomes]
rs12534308	1.00[CHD][hapmap];0.90[TSI][hapmap]
rs12535550	1.00[CHD][hapmap];0.90[TSI][hapmap]
rs12537381	0.82[EUR][1000 genomes]
rs13310169	0.82[EUR][1000 genomes]
rs1514103	0.83[EUR][1000 genomes]
rs1601913	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs1606624	0.83[EUR][1000 genomes]
rs1606625	0.83[EUR][1000 genomes]
rs1606626	0.83[EUR][1000 genomes]
rs1606627	0.83[EUR][1000 genomes]
rs1606629	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs17136282	0.83[EUR][1000 genomes]
rs17136284	0.84[EUR][1000 genomes]
rs17153055	0.82[EUR][1000 genomes]
rs17172548	0.82[EUR][1000 genomes]
rs1825941	0.83[EUR][1000 genomes]
rs1825942	0.83[EUR][1000 genomes]
rs1825943	0.83[EUR][1000 genomes]
rs1844165	0.83[EUR][1000 genomes]
rs1849669	0.81[EUR][1000 genomes]
rs1849670	0.83[EUR][1000 genomes]
rs1849671	0.82[CEU][hapmap]
rs1849672	0.82[CEU][hapmap];0.90[TSI][hapmap]
rs1949247	0.83[EUR][1000 genomes]
rs1949248	0.83[EUR][1000 genomes]
rs1949249	0.83[EUR][1000 genomes]
rs1949250	0.83[EUR][1000 genomes]
rs4095658	0.83[EUR][1000 genomes]
rs4495375	0.82[EUR][1000 genomes]
rs4534091	0.82[EUR][1000 genomes]
rs4545043	0.83[EUR][1000 genomes]
rs4599764	0.82[EUR][1000 genomes]
rs4615523	0.82[EUR][1000 genomes]
rs4636158	0.82[EUR][1000 genomes]
rs4948161	0.82[EUR][1000 genomes]
rs4948163	0.82[EUR][1000 genomes]
rs4948170	0.82[EUR][1000 genomes]
rs57079967	0.80[EUR][1000 genomes]
rs57885398	0.82[EUR][1000 genomes]
rs58687975	0.80[EUR][1000 genomes]
rs60974901	0.80[EUR][1000 genomes]
rs66785139	0.83[EUR][1000 genomes]
rs67090516	0.82[EUR][1000 genomes]
rs67192391	0.83[EUR][1000 genomes]
rs67421275	0.84[EUR][1000 genomes]
rs67587774	0.84[EUR][1000 genomes]
rs67635886	0.83[EUR][1000 genomes]
rs67960993	0.84[EUR][1000 genomes]
rs68099949	0.82[EUR][1000 genomes]
rs68161740	0.82[EUR][1000 genomes]
rs68174956	0.84[EUR][1000 genomes]
rs68179256	0.83[EUR][1000 genomes]
rs73343697	0.83[EUR][1000 genomes]
rs7799034	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs7802014	0.82[EUR][1000 genomes]
rs7802180	0.82[EUR][1000 genomes]
rs7804588	0.82[EUR][1000 genomes]
rs7805333	0.82[EUR][1000 genomes]
rs7811082	0.83[EUR][1000 genomes]
rs9642416	0.81[EUR][1000 genomes]
rs9642417	0.82[EUR][1000 genomes]
rs9642614	0.82[EUR][1000 genomes]
rs9642615	0.82[EUR][1000 genomes]
rs9642617	0.82[EUR][1000 genomes]
rs9942610	0.83[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	nsv427783	chr7:56334626-56983646	Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1022563	chr7:56383876-57318888	Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
3	nsv1016255	chr7:56453095-56835595	ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1028678	chr7:56511649-56795206	ZNF genes & repeats Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv538864	chr7:56511649-56795206	ZNF genes & repeats Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1020833	chr7:56511848-57323499	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv538865	chr7:56511848-57323499	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
8	nsv8090	chr7:56511877-56772523	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1017561	chr7:56512618-57334136	Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
10	nsv831009	chr7:56566629-56754313	ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv1030968	chr7:56610656-56835595	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription	TF binding region CpG island lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv888067	chr7:56668557-56727887	ZNF genes & repeats Active TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
13	esv1804304	chr7:56678691-56727029	ZNF genes & repeats Active TSS	TF binding region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv981482	chr7:56695953-56760954	ZNF genes & repeats Active TSS Weak transcription	TF binding region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12535978	LANCL2	cis	cerebellum	SCAN
rs12535978	FES	trans	lymphoblastoid	seeQTL
rs12535978	CHCHD2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:56723000-56723200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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