Variant report

Variant	rs599044
Chromosome Location	chr13:86167653-86167654
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11617618	1.00[ASN][1000 genomes]
rs12427778	0.83[AFR][1000 genomes]
rs12427783	0.83[AFR][1000 genomes]
rs12428684	0.83[AFR][1000 genomes]
rs12429649	0.83[AFR][1000 genomes]
rs12430426	0.83[AFR][1000 genomes]
rs12430599	0.83[AFR][1000 genomes]
rs1337259	1.00[AFR][1000 genomes]
rs1538058	1.00[AFR][1000 genomes]
rs1544138	1.00[AFR][1000 genomes]
rs1544139	1.00[AFR][1000 genomes]
rs17464617	0.89[EUR][1000 genomes]
rs17464708	0.88[EUR][1000 genomes]
rs1753742	0.83[AFR][1000 genomes]
rs1753745	0.83[AFR][1000 genomes]
rs1753769	1.00[AFR][1000 genomes]
rs1753774	1.00[AFR][1000 genomes]
rs1753776	1.00[AFR][1000 genomes]
rs1753777	1.00[AFR][1000 genomes]
rs17647904	1.00[ASN][1000 genomes]
rs17648180	0.83[AFR][1000 genomes]
rs17648227	0.83[AFR][1000 genomes]
rs17648233	0.83[AFR][1000 genomes]
rs17648253	0.83[AFR][1000 genomes]
rs1764942	1.00[AFR][1000 genomes]
rs1764943	1.00[AFR][1000 genomes]
rs1764955	1.00[AFR][1000 genomes]
rs1764956	0.83[AFR][1000 genomes]
rs1764960	0.83[AFR][1000 genomes]
rs1764967	0.83[AFR][1000 genomes]
rs1764973	0.83[AFR][1000 genomes]
rs1799685	0.83[AFR][1000 genomes]
rs1928135	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1928137	0.86[EUR][1000 genomes]
rs2039656	0.83[AFR][1000 genomes]
rs2094606	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2225232	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2770531	1.00[AFR][1000 genomes]
rs2880523	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34620229	0.83[AFR][1000 genomes]
rs4482178	0.88[EUR][1000 genomes]
rs56163498	0.81[EUR][1000 genomes]
rs585324	0.92[ASN][1000 genomes]
rs585377	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs585409	0.97[ASN][1000 genomes]
rs585411	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59540085	0.81[EUR][1000 genomes]
rs614154	0.83[AFR][1000 genomes]
rs622370	0.83[AFR][1000 genomes]
rs636628	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs666061	0.88[EUR][1000 genomes]
rs684789	0.88[EUR][1000 genomes]
rs685535	0.89[EUR][1000 genomes]
rs686872	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs688569	0.89[EUR][1000 genomes]
rs7329796	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7987119	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7987776	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs943920	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9547292	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs992453	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916866	chr13:85505771-86241562	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1050105	chr13:85524968-86218429	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541857	chr13:85524968-86218429	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2752724	chr13:85810499-86320999	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1037563	chr13:85830511-86414012	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1053499	chr13:85959321-86197157	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv541859	chr13:85959321-86197157	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv471162	chr13:85994700-86296819	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv456051	chr13:85994700-86306452	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv562609	chr13:85994700-86306452	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv428608	chr13:86109178-86262577	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs599044	NCRNA00221	trans	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:86165200-86171800	Weak transcription	HMEC	breast
2	chr13:86167000-86172000	Weak transcription	NHEK	skin
3	chr13:86167600-86172000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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