Variant report

Variant	rs11644740
Chromosome Location	chr16:72002308-72002309
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72001943..72003668-chr16:72042372..72044249,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102967	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10500567	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10852505	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs10852507	0.85[ASN][1000 genomes]
rs11075906	0.86[ASN][1000 genomes]
rs11075910	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11639843	0.85[ASN][1000 genomes]
rs11640135	0.82[ASN][1000 genomes]
rs11640722	1.00[LWK][hapmap]
rs11648557	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11861296	0.82[JPT][hapmap]
rs11865456	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12149307	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12149325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12149460	0.82[JPT][hapmap]
rs12149917	0.86[ASN][1000 genomes]
rs12445564	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12445641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12448086	0.86[ASN][1000 genomes]
rs12708919	1.00[CHB][hapmap]
rs12921279	0.85[ASN][1000 genomes]
rs12921459	0.86[ASN][1000 genomes]
rs12927691	0.85[ASN][1000 genomes]
rs12934512	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs13330178	0.82[ASN][1000 genomes]
rs17357420	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17358402	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2288030	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs2878494	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs34029919	0.85[ASN][1000 genomes]
rs34101687	0.85[ASN][1000 genomes]
rs34664834	0.89[ASN][1000 genomes]
rs35028754	0.82[ASN][1000 genomes]
rs35209006	0.82[ASN][1000 genomes]
rs35404791	0.85[ASN][1000 genomes]
rs35595148	0.82[ASN][1000 genomes]
rs36182990	0.85[ASN][1000 genomes]
rs3751820	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4528577	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4788568	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4788575	0.85[JPT][hapmap]
rs4788579	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs71384781	0.82[ASN][1000 genomes]
rs71384782	0.85[ASN][1000 genomes]
rs71386939	0.89[ASN][1000 genomes]
rs71386940	0.89[ASN][1000 genomes]
rs71386942	0.85[ASN][1000 genomes]
rs7188591	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7191441	0.84[EUR][1000 genomes]
rs7191463	0.83[EUR][1000 genomes]
rs7191717	0.87[CEU][hapmap];0.92[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs7191848	0.85[ASN][1000 genomes]
rs7195072	0.87[CEU][hapmap]
rs7195988	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7197486	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7198834	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7202840	1.00[CHB][hapmap]
rs72787018	0.81[EUR][1000 genomes]
rs72803749	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72803753	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72803757	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72803761	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73586164	0.86[ASN][1000 genomes]
rs8049508	0.85[ASN][1000 genomes]
rs8050058	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs8051878	1.00[CHB][hapmap]
rs8052358	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9939911	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs9940234	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
9	nsv521097	chr16:72001136-72002308	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11644740	PDP2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:71999600-72010600	Weak transcription	Liver	Liver
2	chr16:71999800-72003200	Weak transcription	HepG2	liver

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