Variant report

Variant	rs6580126
Chromosome Location	chr5:154395158-154395159
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1603404	0.90[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2431154	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2431156	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2453756	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2560040	0.91[YRI][hapmap]
rs286599	0.81[ASN][1000 genomes]
rs286601	0.95[CEU][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs286615	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs286616	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs286619	0.90[ASW][hapmap];0.91[CHB][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs286620	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7443026	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883058	chr5:154375465-154432580	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	esv11005	chr5:154393341-154398169	Bivalent/Poised TSS Active TSS Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6580126	MFAP3	cis	cerebellum	SCAN
rs6580126	HAVCR1	cis	cerebellum	SCAN
rs6580126	MFAP3	cis	parietal	SCAN
rs6580126	TIMD4	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154393600-154403000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:154394800-154395600	Weak transcription	GM12878-XiMat	blood

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Input of quick search could be:

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

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