Variant report

Variant	rs1534556
Chromosome Location	chr4:92259485-92259486
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1406316	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap]
rs1528564	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1528572	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1528573	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1528575	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1528576	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1528577	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1528578	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1528581	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1609321	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1609322	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1609323	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1881454	0.86[CEU][hapmap]
rs1881455	1.00[JPT][hapmap]
rs1919226	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1919227	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2178222	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28816531	0.83[EUR][1000 genomes]
rs3762827	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4308338	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs4524348	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4593093	0.83[CEU][hapmap]
rs6532289	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6532290	0.83[CEU][hapmap]
rs6532291	0.89[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs6532292	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6532293	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap]
rs6532299	0.87[CEU][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6532301	0.80[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap]
rs6816636	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6816883	0.81[CEU][hapmap]
rs6817404	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6833290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6834615	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6841781	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs7340864	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7653977	1.00[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs7659326	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7683541	0.83[CEU][hapmap]
rs7696314	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs955500	0.83[CEU][hapmap]
rs9999729	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9999885	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869023	chr4:91940838-92935383	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	esv3448147	chr4:92011533-92275731	Active TSS Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3384271	chr4:92073391-92464275	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1013025	chr4:92183325-92259485	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
5	nsv879566	chr4:92215966-92322333	ZNF genes & repeats Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv879567	chr4:92215966-92413671	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv522208	chr4:92241587-92283771	ZNF genes & repeats Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv1830673	chr4:92241587-92379081	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv879568	chr4:92244300-92429961	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv529020	chr4:92253926-92293482	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1534556	SMARCAD1	cis	cerebellum	SCAN

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

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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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