Variant report

Variant	rs11643269
Chromosome Location	chr16:77377567-77377568
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	chr16:77376619..77379177-chr16:77392341..77394728,2	MCF-7	breast:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11640996	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs11641546	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11866007	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap]
rs12232404	0.92[ASN][1000 genomes]
rs12920358	0.86[ASN][1000 genomes]
rs13332995	0.82[JPT][hapmap]
rs13338913	0.94[ASW][hapmap];0.82[LWK][hapmap];0.93[YRI][hapmap]
rs1366552	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1428836	0.88[ASW][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs1428848	0.82[LWK][hapmap];0.84[MKK][hapmap];0.83[YRI][hapmap]
rs1428851	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1428852	0.89[AFR][1000 genomes]
rs1529496	0.88[ASW][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs1544955	0.85[AFR][1000 genomes]
rs166673	0.83[ASW][hapmap]
rs17713161	0.90[CHB][hapmap];0.93[CHD][hapmap]
rs17770036	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs17770042	0.90[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs1971752	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1981983	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs274534	0.81[CHB][hapmap]
rs274539	0.82[ASW][hapmap];0.81[CHB][hapmap];0.86[YRI][hapmap]
rs28634341	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59718928	0.81[ASN][1000 genomes]
rs62043573	0.91[ASN][1000 genomes]
rs62043574	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs62043575	0.90[ASN][1000 genomes]
rs62044891	0.81[ASN][1000 genomes]
rs6564426	0.83[ASN][1000 genomes]
rs6564427	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.80[ASN][1000 genomes]
rs6564428	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6564430	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6564431	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6564432	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7185277	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7199634	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs7202576	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7206250	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs8044883	0.88[ASW][hapmap];0.84[LWK][hapmap];0.93[YRI][hapmap]
rs8049128	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8050093	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8050620	0.91[AFR][1000 genomes]
rs8053510	0.92[ASN][1000 genomes]
rs8059032	0.94[ASW][hapmap];0.81[LWK][hapmap];0.93[YRI][hapmap]
rs8063520	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs891132	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs954044	0.81[CHB][hapmap]
rs965382	0.81[CHB][hapmap]
rs9674420	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs9938049	0.91[ASN][1000 genomes]
rs998014	0.94[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055234	chr16:77003426-77467286	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1065048	chr16:77003426-77675163	Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	esv2830376	chr16:77014551-77658185	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv1065149	chr16:77032082-77671890	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv1062349	chr16:77039764-77458731	Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv542967	chr16:77039764-77458731	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv1056676	chr16:77139682-77854848	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
8	nsv1066258	chr16:77229953-77521919	Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv542968	chr16:77229953-77521919	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	esv2761916	chr16:77277005-77555833	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1059194	chr16:77281068-77745928	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv542969	chr16:77281068-77745928	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv934211	chr16:77281069-77396084	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv1065714	chr16:77285659-77385518	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv457541	chr16:77353973-77389002	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv573124	chr16:77353973-77389002	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv2751613	chr16:77373039-77444872	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11643269	ADAMTS18	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:77329200-77389800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr16:77359400-77392800	Weak transcription	HUVEC	blood vessel
3	chr16:77365000-77383600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr16:77373000-77377800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr16:77374200-77379400	Weak transcription	Brain Hippocampus Middle	brain
6	chr16:77377200-77378200	Weak transcription	Ovary	ovary
7	chr16:77377400-77378200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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