Variant report

Variant	rs12925901
Chromosome Location	chr16:71991135-71991136
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	chr16:71924634..71926164-chr16:71990513..71992754,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1035543	0.90[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10492825	0.90[CHB][hapmap]
rs10852506	0.85[ASN][1000 genomes]
rs10852508	0.91[ASN][1000 genomes]
rs10852509	0.85[CHB][hapmap]
rs11647844	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11647947	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12149869	0.86[AFR][1000 genomes]
rs12149877	0.83[AFR][1000 genomes]
rs12445043	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12445713	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12447423	0.91[ASN][1000 genomes]
rs12448111	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12600163	0.90[JPT][hapmap]
rs12708920	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12708921	0.82[AFR][1000 genomes]
rs12708922	0.82[AFR][1000 genomes]
rs12919947	0.81[ASN][1000 genomes]
rs12921355	0.90[CHB][hapmap]
rs12926353	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12926408	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs12927381	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13332180	0.85[JPT][hapmap]
rs16973520	0.81[CHB][hapmap];0.88[CHD][hapmap];0.86[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs17286411	0.81[JPT][hapmap]
rs2291947	0.90[JPT][hapmap]
rs2303220	1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs28629271	0.81[AFR][1000 genomes]
rs2878406	0.91[ASN][1000 genomes]
rs4462592	0.91[ASN][1000 genomes]
rs4538017	0.90[JPT][hapmap]
rs4788567	0.90[JPT][hapmap]
rs58114621	0.91[ASN][1000 genomes]
rs58609735	0.86[ASN][1000 genomes]
rs60075093	0.80[ASN][1000 genomes]
rs6499553	0.81[AFR][1000 genomes]
rs7186518	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7186712	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046159	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8046703	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8047643	0.81[AFR][1000 genomes]
rs8051124	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8051364	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8052028	0.89[ASN][1000 genomes]
rs8053217	0.81[AFR][1000 genomes]
rs8053891	0.85[CHB][hapmap];0.96[YRI][hapmap]
rs8055242	0.90[CHB][hapmap]
rs952159	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs952160	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9889100	0.88[ASN][1000 genomes]
rs9921705	0.91[ASN][1000 genomes]
rs9925462	0.85[CHB][hapmap];0.83[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs9928413	0.85[CHB][hapmap];0.83[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs9930930	0.82[AFR][1000 genomes]
rs9938025	0.81[CHB][hapmap];0.83[LWK][hapmap];0.96[YRI][hapmap]

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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	nsv572950	chr16:71988728-72020323	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12925901	TXNL4B	cis	parietal	SCAN
rs12925901	SLC9A5	cis	cerebellum	SCAN

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	chr16:71969600-71999200	Weak transcription	Liver	Liver
3	chr16:71989600-71995000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr16:71989800-71991200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr16:71990200-71991200	Enhancers	GM12878-XiMat	blood
6	chr16:71990400-71991200	Enhancers	Primary B cells from cord blood	blood
7	chr16:71990600-71993600	Weak transcription	Primary B cells from peripheral blood	blood

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