Variant report

Variant	rs1408041
Chromosome Location	chr11:34516984-34516985
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	chr11:34514573..34518104-chr11:34518598..34523939,6	K562	blood:
2	chr11:34516973..34519937-chr11:34521285..34524160,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1008491	0.92[ASN][1000 genomes]
rs10836230	1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs10836234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11032661	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11032667	0.81[ASN][1000 genomes]
rs11032669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11032670	0.81[ASN][1000 genomes]
rs11032671	0.81[ASN][1000 genomes]
rs11032682	0.89[ASN][1000 genomes]
rs11032695	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11032718	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11032722	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11032723	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11032724	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11032726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11032728	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12361866	0.81[ASN][1000 genomes]
rs12790004	0.81[ASN][1000 genomes]
rs12790145	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12790378	0.81[ASN][1000 genomes]
rs12793666	0.89[ASN][1000 genomes]
rs12797675	0.96[CEU][hapmap]
rs12804506	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12804689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12806377	0.81[ASN][1000 genomes]
rs12807961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12808450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1535719	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17269903	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17269931	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17352313	0.81[ASN][1000 genomes]
rs2146962	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231825	0.96[CEU][hapmap]
rs2231828	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2420386	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34329347	0.89[ASN][1000 genomes]
rs34366473	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34533645	0.89[ASN][1000 genomes]
rs34901344	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35725681	0.89[ASN][1000 genomes]
rs475043	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs494024	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs499406	0.84[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs508370	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs511895	0.81[CEU][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs524167	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs533425	0.81[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55898107	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs560807	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59090359	0.81[ASN][1000 genomes]
rs66679411	0.89[ASN][1000 genomes]
rs737254	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs873466	0.81[ASN][1000 genomes]
rs910089	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	esv2761661	chr11:34513932-34519578	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv897211	chr11:34514941-34609541	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1408041	CAT	Cis_1M	lymphoblastoid	RTeQTL
rs1408041	CAT	cis	Whole Blood	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34512200-34517200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr11:34516600-34517000	Enhancers	Lung	lung
3	chr11:34516600-34517200	Enhancers	HepG2	liver
4	chr11:34516800-34517000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:34516800-34517400	Enhancers	HMEC	breast
6	chr11:34516800-34517600	Enhancers	Hela-S3	cervix
7	chr11:34516800-34519000	Enhancers	Fetal Lung	lung

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