Variant report

Variant	rs17648180
Chromosome Location	chr13:86275588-86275589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11617680	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11619198	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12427778	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12427783	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12428684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12429649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12430426	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12430599	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1337258	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1337259	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1415403	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1538055	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1538058	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1544138	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1544139	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17080097	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17080098	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17080100	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17080101	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1752903	0.82[AMR][1000 genomes]
rs1753740	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1753742	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1753745	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1753765	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1753769	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1753774	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1753776	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1753777	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17648227	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17648233	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17648253	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1764941	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1764942	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1764943	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1764950	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1764955	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1764956	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1764957	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1764960	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1764967	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1764973	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1799685	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1928135	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2027234	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2039656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2094606	0.83[AFR][1000 genomes]
rs2225232	0.83[AFR][1000 genomes]
rs2343057	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2770531	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2880523	0.83[AFR][1000 genomes]
rs34620229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55768080	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs585377	0.83[AFR][1000 genomes]
rs587347	0.85[EUR][1000 genomes]
rs587403	0.85[EUR][1000 genomes]
rs587419	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs590505	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs599044	0.83[AFR][1000 genomes]
rs599802	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs603177	0.85[EUR][1000 genomes]
rs610472	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs614154	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs622370	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs636628	0.83[AFR][1000 genomes]
rs664674	0.85[EUR][1000 genomes]
rs677195	0.85[EUR][1000 genomes]
rs680523	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs686872	0.83[AFR][1000 genomes]
rs7329796	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs74102085	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs74102094	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74102095	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs74102097	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7491718	0.85[EUR][1000 genomes]
rs7491907	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7987119	0.83[AFR][1000 genomes]
rs7987776	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs943920	0.83[AFR][1000 genomes]
rs9547292	0.83[AFR][1000 genomes]
rs9547317	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9594049	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9602814	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9671144	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9671154	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv900733	chr13:86192376-86309366	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv832668	chr13:86234885-86364254	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv1044417	chr13:86239152-86344862	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17648180	NCRNA00221	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:86273000-86275600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:86274000-86313200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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