Variant report

Variant	rs2076874
Chromosome Location	chr6:64153691-64153692
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	chr6:64153026..64155421-chr6:64281579..64283450,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266680	Chromatin interaction
ENSG00000112245	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10755410	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10806206	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10943902	0.83[JPT][hapmap]
rs1197902	0.83[JPT][hapmap]
rs1197905	0.83[JPT][hapmap]
rs12196062	0.81[ASN][1000 genomes]
rs1322415	0.84[JPT][hapmap]
rs1322416	0.83[JPT][hapmap]
rs1570315	0.83[JPT][hapmap]
rs1620671	0.83[JPT][hapmap]
rs1630182	0.83[JPT][hapmap]
rs1681942	0.83[JPT][hapmap]
rs1681946	0.83[JPT][hapmap]
rs1681947	0.83[JPT][hapmap]
rs1681957	0.83[JPT][hapmap]
rs1723535	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1741801	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1744147	0.86[JPT][hapmap]
rs1744152	0.83[JPT][hapmap]
rs1779747	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1779748	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1969717	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2096346	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146149	0.83[JPT][hapmap]
rs2146150	0.83[JPT][hapmap]
rs2186011	0.81[ASN][1000 genomes]
rs2622274	0.83[JPT][hapmap]
rs2622281	0.83[JPT][hapmap]
rs2622286	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622307	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2753062	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2753066	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2758224	0.83[JPT][hapmap]
rs2758225	0.83[JPT][hapmap]
rs2758237	0.83[JPT][hapmap]
rs2758259	0.83[JPT][hapmap]
rs2800017	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800018	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800023	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800027	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800028	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2800048	0.81[JPT][hapmap]
rs2800049	0.83[JPT][hapmap]
rs4358600	0.81[CEU][hapmap];0.82[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4445042	0.81[EUR][1000 genomes]
rs4543353	0.83[JPT][hapmap]
rs4710254	0.81[EUR][1000 genomes]
rs4710255	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4710430	0.82[ASN][1000 genomes]
rs6919709	0.81[EUR][1000 genomes]
rs6929702	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6938965	0.83[JPT][hapmap]
rs6939983	0.81[ASN][1000 genomes]
rs7742595	0.84[ASN][1000 genomes]
rs7745873	0.82[ASN][1000 genomes]
rs7763834	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9294196	0.81[EUR][1000 genomes]
rs9294197	0.81[EUR][1000 genomes]
rs9294198	0.81[EUR][1000 genomes]
rs9294206	0.81[EUR][1000 genomes]
rs9294215	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9294234	0.83[JPT][hapmap]
rs9294269	0.83[JPT][hapmap]
rs9341841	0.81[EUR][1000 genomes]
rs9344090	0.81[EUR][1000 genomes]
rs9344129	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344137	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9344168	0.81[ASN][1000 genomes]
rs9350913	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9352960	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9353016	0.82[JPT][hapmap]
rs9359467	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9361762	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9361767	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9361779	0.84[ASN][1000 genomes]
rs9361838	0.83[JPT][hapmap]
rs9449233	0.81[EUR][1000 genomes]
rs9449291	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs9449297	0.82[ASN][1000 genomes]
rs9449312	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019831	chr6:63279677-64230736	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2076874	LGSN	cis	Whole Blood	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:64146600-64158000	Weak transcription	Hela-S3	cervix
2	chr6:64152200-64157200	Weak transcription	Liver	Liver
3	chr6:64153000-64154600	Weak transcription	HepG2	liver
4	chr6:64153600-64154000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr6:64153600-64157000	Weak transcription	A549	lung

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