Variant report

Variant	rs10797042
Chromosome Location	chr1:159463301-159463302
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10157356	0.91[AFR][1000 genomes]
rs10157831	0.89[AFR][1000 genomes]
rs10159061	0.91[AFR][1000 genomes]
rs10752629	0.91[AFR][1000 genomes]
rs10797038	0.91[AFR][1000 genomes]
rs10797039	0.91[AFR][1000 genomes]
rs10797040	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10797041	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908721	0.85[LWK][hapmap];0.88[MKK][hapmap]
rs10908728	0.91[AFR][1000 genomes]
rs10908729	0.87[AFR][1000 genomes]
rs11265207	0.91[AFR][1000 genomes]
rs11265208	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11265210	0.91[AFR][1000 genomes]
rs11265211	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265212	0.86[AFR][1000 genomes]
rs11265215	0.94[AFR][1000 genomes]
rs12124964	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12126265	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12127293	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12131358	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12132709	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12133664	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133727	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12135090	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12141291	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12409528	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12750941	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12756262	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28420559	0.85[AMR][1000 genomes]
rs34000798	0.87[EUR][1000 genomes]
rs4133289	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4284261	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4325129	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4403627	0.86[AFR][1000 genomes]
rs4415558	0.91[AFR][1000 genomes]
rs4491058	0.85[LWK][hapmap];0.86[MKK][hapmap]
rs4532833	0.91[AFR][1000 genomes]
rs4573514	0.90[AFR][1000 genomes]
rs4590667	0.91[AFR][1000 genomes]
rs4641306	0.91[AFR][1000 genomes]
rs4656827	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821536	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61821537	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427473	0.82[LWK][hapmap]
rs6427475	0.91[AFR][1000 genomes]
rs6664431	0.91[AFR][1000 genomes]
rs6664777	0.91[AFR][1000 genomes]
rs6664977	0.91[AFR][1000 genomes]
rs6664991	0.91[AFR][1000 genomes]
rs6672096	0.90[AFR][1000 genomes]
rs6677055	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678381	0.90[JPT][hapmap]
rs6680456	0.95[AFR][1000 genomes]
rs6684416	0.91[AFR][1000 genomes]
rs6687518	0.94[AFR][1000 genomes]
rs6688273	0.87[AFR][1000 genomes]
rs6695508	0.91[AFR][1000 genomes]
rs6698250	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7518439	0.91[AFR][1000 genomes]
rs7519020	0.81[AMR][1000 genomes]
rs7525975	0.95[AFR][1000 genomes]
rs7540007	0.85[AMR][1000 genomes]
rs7541480	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7544275	0.91[AFR][1000 genomes]
rs7551346	0.88[EUR][1000 genomes]
rs7555008	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9628657	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005195	chr1:159452759-159910337	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10797042	SHE	cis	cerebellum	SCAN
rs10797042	THBS3	cis	cerebellum	SCAN
rs10797042	SCAMP3	cis	cerebellum	SCAN
rs10797042	CD84	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:159461800-159463400	Enhancers	Muscle Satellite Cultured Cells	--
2	chr1:159461800-159463400	Enhancers	Hela-S3	cervix
3	chr1:159461800-159463400	Enhancers	HUVEC	blood vessel
4	chr1:159461800-159463400	Enhancers	Osteobl	bone
5	chr1:159463000-159463400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:159463200-159463400	Enhancers	A549	lung

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