Variant report

Variant	rs2888540
Chromosome Location	chr7:147675432-147675433
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10240503	0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs10243319	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10280388	0.83[CHB][hapmap];0.88[MEX][hapmap]
rs10952722	0.83[CHB][hapmap]
rs10952723	0.83[CHB][hapmap];0.84[MEX][hapmap]
rs11766926	0.95[CEU][hapmap]
rs11773362	0.96[CEU][hapmap];0.90[GIH][hapmap]
rs12531913	0.84[MEX][hapmap]
rs12667149	0.83[CHB][hapmap];0.84[MEX][hapmap]
rs12671605	0.83[CHB][hapmap]
rs12674206	0.83[CHB][hapmap]
rs12703988	0.83[CHB][hapmap]
rs13229141	0.86[CEU][hapmap]
rs1922879	0.87[CEU][hapmap]
rs1990057	0.88[MEX][hapmap]
rs2254307	0.88[YRI][hapmap]
rs2373277	0.81[YRI][hapmap]
rs2373283	0.88[CEU][hapmap]
rs2373284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527055	0.88[MEX][hapmap]
rs2527066	0.88[MEX][hapmap]
rs2707583	0.88[MEX][hapmap]
rs2707593	0.92[YRI][hapmap]
rs2710143	0.88[MEX][hapmap]
rs2710144	0.88[MEX][hapmap]
rs2888541	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4296960	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4725756	0.92[CEU][hapmap];0.90[GIH][hapmap]
rs4726900	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap]
rs6944674	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6960266	0.82[CHB][hapmap]
rs6965400	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6979577	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023913	chr7:147521075-147806318	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1026058	chr7:147521109-147783042	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv539179	chr7:147521109-147783042	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv934002	chr7:147521110-147807705	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1017610	chr7:147523752-147806427	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv889399	chr7:147643923-147712471	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv889400	chr7:147650411-147712471	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2888540	SMARCD3	cis	parietal	SCAN
rs2888540	EZH2	cis	cerebellum	SCAN
rs2888540	WDR86	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:147674600-147676000	Enhancers	Fetal Lung	lung

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