Variant report

Variant	rs1029091
Chromosome Location	chr6:64444457-64444458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10943958	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10944026	0.89[ASN][1000 genomes]
rs13197043	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13199206	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13199805	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13208965	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13216525	0.80[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs1412864	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1412865	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3800489	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3800490	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4351235	1.00[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4634434	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4710256	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4710257	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4710436	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4710439	0.89[ASN][1000 genomes]
rs58429651	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs756274	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7762059	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs7764184	0.88[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	nsv830674	chr6:64355412-64535801	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1022376	chr6:64386826-64445195	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1029091	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64424200-64450400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:64436400-64444600	Weak transcription	HepG2	liver
3	chr6:64436800-64445400	Weak transcription	Primary T cells from cord blood	blood
4	chr6:64437400-64459600	Weak transcription	Aorta	Aorta
5	chr6:64437800-64445000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:64442000-64451800	Weak transcription	Fetal Intestine Small	intestine
7	chr6:64442000-64451800	Weak transcription	Small Intestine	intestine
8	chr6:64442200-64444600	Weak transcription	NHEK	skin
9	chr6:64442400-64445400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:64442400-64450200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:64443000-64444600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:64443200-64444600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:64443200-64444600	Weak transcription	HMEC	breast
14	chr6:64443600-64444600	Weak transcription	Hela-S3	cervix
15	chr6:64443800-64449200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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