Variant report

Variant	rs3853676
Chromosome Location	chr11:57893967-57893968
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:57893156..57895554-chr11:57899477..57901378,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1031360	0.88[CEU][hapmap]
rs10896701	0.92[CEU][hapmap]
rs11229264	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1155858	0.90[JPT][hapmap]
rs11600060	0.88[CEU][hapmap]
rs11601841	0.88[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs11604473	0.88[CEU][hapmap];0.81[JPT][hapmap]
rs11604630	0.88[CEU][hapmap]
rs12283722	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12788387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs12804808	0.90[JPT][hapmap]
rs12805812	0.88[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1376489	0.84[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs1447166	0.80[CHB][hapmap]
rs17152364	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap]
rs17152376	0.88[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs1814059	0.88[CEU][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes]
rs1868881	1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2245676	0.88[CEU][hapmap]
rs2441970	0.86[CEU][hapmap]
rs2443441	0.88[CEU][hapmap]
rs36104388	0.81[EUR][1000 genomes]
rs3862656	0.82[EUR][1000 genomes]
rs4509781	0.84[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes]
rs4939180	0.88[CEU][hapmap]
rs56298140	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61902775	0.80[EUR][1000 genomes]
rs61902797	0.82[EUR][1000 genomes]
rs61902798	0.83[EUR][1000 genomes]
rs61902799	0.83[EUR][1000 genomes]
rs7113760	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs7120102	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs7120442	0.88[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs7130381	0.82[JPT][hapmap];0.83[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930102	0.84[GIH][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap]
rs7934149	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7934184	0.88[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7935428	0.88[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap]
rs7938062	0.88[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs7945154	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs7948507	0.82[EUR][1000 genomes]
rs7949119	0.82[EUR][1000 genomes]
rs7949558	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs895660	0.92[CEU][hapmap]
rs921445	0.82[JPT][hapmap]
rs930703	0.88[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv1054205	chr11:57544264-58358509	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv897589	chr11:57623815-58052357	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv832165	chr11:57806024-58009076	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv832166	chr11:57852031-58006189	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3853676	UBE2L6	cis	parietal	SCAN
rs3853676	SYT7	cis	cerebellum	SCAN
rs3853676	OR5M1	cis	cerebellum	SCAN
rs3853676	OR4D6	cis	cerebellum	SCAN
rs3853676	DDB1	cis	cerebellum	SCAN
rs3853676	PRG3	cis	parietal	SCAN
rs3853676	MS4A2	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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