Variant report

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1033637	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10489624	0.89[MKK][hapmap]
rs2076776	0.93[AMR][1000 genomes]
rs594105	0.89[MKK][hapmap]
rs601662	0.90[MEX][hapmap];0.84[AMR][1000 genomes]
rs603154	0.86[AMR][1000 genomes]
rs622299	0.82[MEX][hapmap];0.85[AMR][1000 genomes]
rs635922	0.86[AMR][1000 genomes]
rs647513	0.92[AMR][1000 genomes]
rs647962	0.80[ASW][hapmap];0.91[AMR][1000 genomes]
rs648939	0.92[AMR][1000 genomes]
rs649798	0.92[AMR][1000 genomes]
rs652785	0.89[MKK][hapmap]
rs658444	0.92[AMR][1000 genomes]
rs659330	0.92[AMR][1000 genomes]
rs663352	0.83[AFR][1000 genomes]
rs664142	0.91[MEX][hapmap];0.90[AMR][1000 genomes]
rs668551	0.80[ASW][hapmap];0.91[MEX][hapmap];0.92[AMR][1000 genomes]
rs669444	0.85[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs671137	0.85[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682584	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv1000266	chr1:57291371-57319480	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1033729	BSND	cis	parietal	SCAN
rs1033729	USP24	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57314400-57317400	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr1:57314600-57317000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:57314800-57316400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr1:57315000-57316400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:57315200-57316400	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr1:57315200-57317000	Enhancers	Brain Germinal Matrix	brain
7	chr1:57315600-57316400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr1:57315800-57320000	Enhancers	HepG2	liver
9	chr1:57316200-57316400	Weak transcription	Fetal Brain Female	brain

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