Variant report

Variant	rs2431156
Chromosome Location	chr5:154410863-154410864
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10057198	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1603404	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431154	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286601	0.95[CEU][hapmap];0.89[JPT][hapmap]
rs286615	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs286616	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs286619	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs286620	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs286626	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs286630	0.82[ASN][1000 genomes]
rs286631	0.82[ASN][1000 genomes]
rs287121	0.82[ASN][1000 genomes]
rs287123	0.82[ASN][1000 genomes]
rs287124	0.82[ASN][1000 genomes]
rs28775325	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6580126	0.90[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs664586	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7443026	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv3374550	chr5:154403808-154421409	Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
3	esv3410951	chr5:154403808-154427370	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
4	esv3348246	chr5:154410859-154413982	Weak transcription Enhancers	n/a	n/a	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2431156	MFAP3	cis	cerebellum	SCAN
rs2431156	TIMD4	cis	cerebellum	SCAN
rs2431156	HAVCR1	cis	cerebellum	SCAN
rs2431156	MFAP3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154404000-154413400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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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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