Variant report

Variant	rs7143565
Chromosome Location	chr14:78887710-78887711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10131390	0.94[CHB][hapmap]
rs10135795	0.88[CHB][hapmap]
rs10136254	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10139602	0.94[CHB][hapmap];0.89[JPT][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11851331	0.82[CHB][hapmap]
rs12887343	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12893958	0.88[CEU][hapmap]
rs12897526	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs17107534	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs17107537	0.81[AFR][1000 genomes]
rs17107573	0.86[YRI][hapmap]
rs2110426	0.88[CEU][hapmap];0.84[JPT][hapmap]
rs2110427	0.88[CEU][hapmap]
rs2215837	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs6574440	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6574441	0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7144816	0.84[JPT][hapmap]
rs7149345	1.00[CEU][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7156727	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7157332	0.83[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8006308	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8007953	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8008554	0.94[CHB][hapmap]
rs8008709	0.94[CHB][hapmap]
rs8017044	0.88[CEU][hapmap];0.86[TSI][hapmap]
rs965408	0.88[CEU][hapmap];0.86[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832837	chr14:78766805-78946526	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	esv2757577	chr14:78875607-78912967	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
3	esv2760000	chr14:78875607-79173528	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7143565	LIN52	cis	parietal	SCAN
rs7143565	HEATR4	cis	parietal	SCAN
rs7143565	HEATR4	cis	cerebellum	SCAN
rs7143565	NPC2	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78882400-78888000	Weak transcription	Brain Germinal Matrix	brain
2	chr14:78884600-78888200	Weak transcription	GM12878-XiMat	blood
3	chr14:78886400-78898200	Weak transcription	Fetal Brain Male	brain

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