Variant report

Variant	rs12926041
Chromosome Location	chr16:71978645-71978646
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:71977547..71980490-chr16:71985780..71987589,2	K562	blood:
2	chr16:71968291..71970171-chr16:71976434..71979180,2	K562	blood:
3	chr16:71967092..71968643-chr16:71978130..71979874,2	MCF-7	breast:
4	chr16:71927647..71930495-chr16:71978328..71980401,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IST1-2	chr16:71978208-71978654	ucscGeneNc_uc002fco_1

Variant related genes	Relation type
ENSG00000182149	Chromatin interaction
ENSG00000102984	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11075908	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11075911	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11648353	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11648530	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11649672	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12102548	0.91[EUR][1000 genomes]
rs12444829	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12447045	0.89[EUR][1000 genomes]
rs12449139	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12599192	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12921084	0.88[EUR][1000 genomes]
rs12926300	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12930744	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12935795	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13329779	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1834034	0.86[EUR][1000 genomes]
rs1834035	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1981874	0.88[EUR][1000 genomes]
rs2008675	0.88[EUR][1000 genomes]
rs2018384	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2288029	0.89[EUR][1000 genomes]
rs2288031	0.90[EUR][1000 genomes]
rs2335709	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2335710	0.90[EUR][1000 genomes]
rs2335711	0.88[EUR][1000 genomes]
rs2335712	0.89[EUR][1000 genomes]
rs2335713	0.89[EUR][1000 genomes]
rs2335714	0.90[EUR][1000 genomes]
rs2335715	0.86[EUR][1000 genomes]
rs28697038	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2878492	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3794692	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4788447	0.86[EUR][1000 genomes]
rs4788449	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4788562	0.83[EUR][1000 genomes]
rs4788564	0.87[EUR][1000 genomes]
rs4788566	0.87[EUR][1000 genomes]
rs4788570	0.90[EUR][1000 genomes]
rs4788571	0.90[EUR][1000 genomes]
rs4788573	0.90[EUR][1000 genomes]
rs4788576	0.93[EUR][1000 genomes]
rs4788581	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4788582	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4788584	0.91[EUR][1000 genomes]
rs4788585	0.91[EUR][1000 genomes]
rs62053803	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6499545	0.87[EUR][1000 genomes]
rs6499551	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6499552	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7184437	0.86[EUR][1000 genomes]
rs7184486	0.85[EUR][1000 genomes]
rs7187129	0.84[EUR][1000 genomes]
rs7193731	0.90[EUR][1000 genomes]
rs7204708	0.91[EUR][1000 genomes]
rs7205154	0.85[EUR][1000 genomes]
rs8044342	0.87[EUR][1000 genomes]
rs8046859	0.87[EUR][1000 genomes]
rs8050488	0.83[EUR][1000 genomes]
rs8050651	0.88[EUR][1000 genomes]
rs8051038	0.87[EUR][1000 genomes]
rs8054111	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8054175	0.88[EUR][1000 genomes]
rs8054403	0.88[EUR][1000 genomes]
rs8057124	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8058118	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8059053	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8062946	0.94[EUR][1000 genomes]
rs8063324	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8063403	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9302631	0.94[EUR][1000 genomes]
rs9302632	0.93[EUR][1000 genomes]
rs9806882	0.93[EUR][1000 genomes]
rs9806905	0.83[EUR][1000 genomes]
rs9888748	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9889011	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9921412	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9932922	0.81[EUR][1000 genomes]
rs9934803	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9934812	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9937936	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3347477	chr16:71555148-71985177	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv1056439	chr16:71916498-72051144	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv1055854	chr16:71922144-72082886	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv906893	chr16:71922663-71988728	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
6	nsv516948	chr16:71965725-71988728	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a
7	nsv833273	chr16:71971805-72152854	Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	esv3332392	chr16:71977901-71980699	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
12	esv3382933	chr16:71977969-71980182	Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
13	esv3397820	chr16:71978076-71980624	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71968800-71995400	Weak transcription	Right Atrium	heart
2	chr16:71969600-71990600	Weak transcription	Adipose Nuclei	Adipose
3	chr16:71969600-71999200	Weak transcription	Liver	Liver
4	chr16:71969800-71980600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr16:71977400-71978800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr16:71977400-71980000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr16:71977600-71978800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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