Variant report

Variant	rs601662
Chromosome Location	chr1:57333759-57333760
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:57327047..57329042-chr1:57332021..57334016,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1033729	0.90[MEX][hapmap];0.84[AMR][1000 genomes]
rs1360151	0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1411012	0.87[ASN][1000 genomes]
rs1418471	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2076776	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284951	0.87[ASN][1000 genomes]
rs3738563	0.98[ASN][1000 genomes]
rs603154	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61766985	0.98[ASN][1000 genomes]
rs622299	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629799	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs634144	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs635922	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636879	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647513	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs647962	0.96[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648939	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs649798	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658444	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6588656	0.87[ASN][1000 genomes]
rs6588657	0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs659330	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662377	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664142	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669054	0.98[ASN][1000 genomes]
rs668551	0.92[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs669444	0.86[MEX][hapmap];0.85[AMR][1000 genomes]
rs6696110	0.85[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs671137	0.86[MEX][hapmap];0.85[AMR][1000 genomes]
rs682584	0.85[AMR][1000 genomes]
rs706476	1.00[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7520004	0.85[ASN][1000 genomes]
rs7520006	0.85[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	nsv508215	chr1:57319460-57351150	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs601662	BSND	cis	parietal	SCAN
rs601662	USP24	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57324400-57339000	Weak transcription	HepG2	liver
2	chr1:57332200-57333800	Enhancers	Muscle Satellite Cultured Cells	--
3	chr1:57332200-57334600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:57332200-57336000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:57332400-57343000	Strong transcription	Liver	Liver
6	chr1:57332600-57334400	Enhancers	Osteobl	bone
7	chr1:57332600-57336200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:57332600-57336200	Enhancers	NHDF-Ad	bronchial
9	chr1:57332800-57334400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:57333000-57338200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:57333200-57336000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:57333400-57338400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:57333600-57334400	Weak transcription	NHLF	lung
14	chr1:57333600-57338400	Weak transcription	NHEK	skin

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