Variant report

Variant	rs859665
Chromosome Location	chr1:172664442-172664443
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1102709	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1102712	0.95[EUR][1000 genomes]
rs2220728	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2859328	1.00[ASN][1000 genomes]
rs59871679	0.94[EUR][1000 genomes]
rs859649	1.00[ASN][1000 genomes]
rs859652	1.00[ASN][1000 genomes]
rs859653	1.00[ASN][1000 genomes]
rs859654	1.00[ASN][1000 genomes]
rs859666	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	esv3404942	chr1:172662154-172664702	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
2	esv3345794	chr1:172662479-172665027	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
3	esv3404268	chr1:172662879-172664527	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs859665	GPA33	cis	cerebellum	SCAN
rs859665	XCL2	cis	cerebellum	SCAN
rs859665	CREG1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172649000-172667000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:172652400-172666800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:172655800-172673800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:172664200-172664600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:172664200-172666200	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr1:172664400-172666800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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