Variant report

Variant	rs2304777
Chromosome Location	chr2:234227523-234227524
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1000547	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11890336	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11891546	0.83[CHB][hapmap]
rs1965811	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2241873	0.85[TSI][hapmap]
rs2241874	0.85[TSI][hapmap]
rs2241875	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792096	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792097	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792100	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6431305	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6710735	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6745476	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6861	0.80[TSI][hapmap]
rs745498	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7570515	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7608122	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs894100	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584699	chr2:234182240-234255547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2304777	ECEL1	cis	parietal	SCAN
rs2304777	ATG16L1	cis	cerebellum	SCAN
rs2304777	GIGYF2	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234222200-234230200	Weak transcription	GM12878-XiMat	blood
2	chr2:234222600-234229800	Weak transcription	Primary B cells from cord blood	blood
3	chr2:234223600-234245400	Weak transcription	Pancreas	Pancrea
4	chr2:234226000-234227600	Enhancers	Primary B cells from peripheral blood	blood
5	chr2:234226800-234228600	Weak transcription	Fetal Brain Male	brain

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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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