Variant report

Variant	rs7520086
Chromosome Location	chr1:72385590-72385591
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10493488	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10493490	1.00[ASW][hapmap];0.83[CEU][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap]
rs11209871	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11209878	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11209888	1.00[ASW][hapmap];0.89[JPT][hapmap]
rs1155261	0.89[JPT][hapmap]
rs12023418	0.89[JPT][hapmap]
rs12024501	0.89[JPT][hapmap]
rs12029938	1.00[CEU][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs12033580	0.95[EUR][1000 genomes]
rs12034458	0.81[CEU][hapmap];0.94[JPT][hapmap]
rs12035495	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs12040021	0.95[EUR][1000 genomes]
rs12043636	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs12047003	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12047266	0.84[EUR][1000 genomes]
rs17091962	0.80[JPT][hapmap]
rs17091997	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs17092178	0.89[JPT][hapmap]
rs17092217	0.89[JPT][hapmap]
rs1834526	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162238	0.95[EUR][1000 genomes]
rs59416074	0.84[EUR][1000 genomes]
rs6659791	0.95[EUR][1000 genomes]
rs6667732	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs6667747	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs6678735	0.95[JPT][hapmap]
rs6696193	1.00[CEU][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes]
rs6698069	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7528016	0.95[EUR][1000 genomes]
rs7553008	1.00[CEU][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes]
rs9787171	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948821	chr1:72049987-72477221	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1003446	chr1:72060680-72419918	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv817447	chr1:72098815-72558020	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv916783	chr1:72196061-72707953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1007910	chr1:72247302-72543998	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv2762150	chr1:72271227-72395953	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv999162	chr1:72319163-72477496	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv534995	chr1:72319163-72477496	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv428763	chr1:72353556-72499701	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7520086	LRRC40	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:72384000-72388000	Enhancers	Liver	Liver
2	chr1:72385200-72386000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr1:72385400-72386000	Enhancers	H1 Cell Line	embryonic stem cell
4	chr1:72385400-72386000	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:72385400-72386200	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:72385400-72386400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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