Variant report

Variant	rs6777541
Chromosome Location	chr3:159024524-159024525
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10513537	0.82[ASW][hapmap];0.90[GIH][hapmap]
rs10936173	1.00[ASW][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs1122205	0.93[CEU][hapmap]
rs11921343	0.86[CEU][hapmap]
rs11924990	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs13326945	0.86[GIH][hapmap]
rs1349165	0.93[CEU][hapmap]
rs1349166	0.93[CEU][hapmap]
rs1449018	0.93[CEU][hapmap]
rs1449019	0.93[CEU][hapmap]
rs1449025	0.93[CEU][hapmap]
rs1562669	0.93[CEU][hapmap]
rs1823311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1868414	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2017685	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2122147	0.86[ASN][1000 genomes]
rs2365490	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs2365820	0.93[CEU][hapmap]
rs2365821	0.92[CEU][hapmap]
rs6441253	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441254	0.93[CEU][hapmap]
rs6780514	0.86[CEU][hapmap]
rs6781221	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6791853	1.00[ASW][hapmap];0.91[GIH][hapmap]
rs6807305	0.93[CEU][hapmap]
rs6810169	0.93[CEU][hapmap]
rs720397	0.86[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7611870	0.93[CEU][hapmap]
rs7629577	0.93[CEU][hapmap]
rs7629583	0.93[CEU][hapmap]
rs7630467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7639623	0.86[ASN][1000 genomes]
rs9283610	0.87[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9283611	0.93[CEU][hapmap]
rs9290036	0.93[CEU][hapmap]
rs9681445	0.93[CEU][hapmap]
rs9809459	0.93[CEU][hapmap]
rs9820047	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs9821641	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9823822	0.93[CEU][hapmap]
rs9825664	0.93[CEU][hapmap]
rs9827242	0.85[ASN][1000 genomes]
rs9827400	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs9831067	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.80[TSI][hapmap];0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9832614	0.85[CEU][hapmap]
rs9834328	1.00[CHB][hapmap]
rs9834337	0.93[CEU][hapmap]
rs9838646	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];0.83[TSI][hapmap]
rs9839112	1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs9852196	0.86[ASN][1000 genomes]
rs9855118	0.93[CEU][hapmap]
rs9856166	1.00[ASW][hapmap];0.81[CHB][hapmap];0.91[GIH][hapmap]
rs9862769	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9865361	0.86[CEU][hapmap]
rs9867432	0.93[CEU][hapmap]
rs9871574	0.86[CEU][hapmap]
rs9873091	0.93[CEU][hapmap]
rs9874504	0.85[CEU][hapmap]
rs9874862	0.93[CEU][hapmap]
rs9880642	0.90[CHB][hapmap]

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	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv470971	chr3:158590928-159158217	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv998949	chr3:158774806-159394550	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1012602	chr3:158800182-159031618	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6777541	MACC1	trans	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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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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