Variant report

Variant	rs209836
Chromosome Location	chr16:12423557-12423558
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	chr16:12415388..12417131-chr16:12421455..12424382,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11075062	0.85[ASW][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11641317	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11641878	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11648255	0.80[AMR][1000 genomes]
rs11648926	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12595990	0.81[YRI][hapmap]
rs1476117	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs158467	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16959318	0.81[EUR][1000 genomes]
rs16959342	0.80[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs176717	0.83[AMR][1000 genomes]
rs2013951	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs209834	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs209835	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209839	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs209845	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs209849	0.84[AMR][1000 genomes]
rs209850	0.85[AMR][1000 genomes]
rs209853	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs209854	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs209855	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2856766	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2856770	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs31679	0.80[EUR][1000 genomes]
rs476267	0.83[EUR][1000 genomes]
rs4781205	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4781207	0.81[EUR][1000 genomes]
rs4781209	0.85[GIH][hapmap]
rs4781211	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4781214	0.83[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs512286	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs540972	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs544598	0.84[EUR][1000 genomes]
rs544673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6498277	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7184369	0.81[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7185731	0.81[YRI][hapmap]
rs7190509	0.85[GIH][hapmap]
rs7200289	0.80[ASW][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.82[ASN][1000 genomes]
rs7202201	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7203117	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8051010	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs868773	0.85[GIH][hapmap]
rs9284322	0.83[GIH][hapmap]
rs9635495	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv457411	chr16:12363304-12520199	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv571462	chr16:12363304-12520199	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1045385	chr16:12376389-12517006	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542748	chr16:12376389-12517006	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv905349	chr16:12408750-12445863	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv827555	chr16:12413244-12429978	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv571464	chr16:12423557-12449778	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12371400-12456800	Weak transcription	Aorta	Aorta
2	chr16:12404200-12427400	Weak transcription	Primary T cells from cord blood	blood
3	chr16:12405600-12426400	Weak transcription	Lung	lung
4	chr16:12405600-12442400	Weak transcription	Spleen	Spleen
5	chr16:12410000-12456600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr16:12410200-12424400	Weak transcription	Right Atrium	heart
7	chr16:12410200-12464800	Weak transcription	Gastric	stomach
8	chr16:12414400-12431400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr16:12414800-12432000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr16:12415000-12424600	Weak transcription	Esophagus	oesophagus
11	chr16:12415000-12431600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr16:12415400-12435400	Weak transcription	Pancreas	Pancrea
13	chr16:12415600-12425200	Weak transcription	Primary B cells from cord blood	blood
14	chr16:12416000-12423800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr16:12416200-12427600	Weak transcription	Thymus	Thymus
16	chr16:12416800-12438600	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr16:12417800-12424200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr16:12418400-12426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr16:12418400-12433400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr16:12418400-12433400	Weak transcription	Brain Substantia Nigra	brain
21	chr16:12418400-12438400	Weak transcription	Brain Anterior Caudate	brain
22	chr16:12418600-12424600	Weak transcription	Psoas Muscle	Psoas
23	chr16:12421600-12428400	Enhancers	Stomach Smooth Muscle	stomach
24	chr16:12421800-12423800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr16:12421800-12425400	Enhancers	Colon Smooth Muscle	Colon
26	chr16:12422000-12424000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr16:12422000-12432200	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr16:12422400-12424400	Weak transcription	Rectal Smooth Muscle	rectum
29	chr16:12422400-12424400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr16:12422600-12423600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr16:12422600-12425400	Enhancers	GM12878-XiMat	blood
32	chr16:12422800-12424600	Weak transcription	Adipose Nuclei	Adipose
33	chr16:12422800-12424800	Weak transcription	Liver	Liver
34	chr16:12423000-12423600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr16:12423000-12424400	Weak transcription	Fetal Stomach	stomach
36	chr16:12423000-12425000	Enhancers	Left Ventricle	heart
37	chr16:12423000-12425000	Enhancers	Right Ventricle	heart
38	chr16:12423000-12425600	Enhancers	Fetal Heart	heart
39	chr16:12423000-12426800	Enhancers	Fetal Muscle Leg	muscle
40	chr16:12423200-12424600	Weak transcription	Ovary	ovary
41	chr16:12423200-12425400	Genic enhancers	Primary B cells from peripheral blood	blood
42	chr16:12423400-12423800	Enhancers	Fetal Brain Female	brain
43	chr16:12423400-12423800	Enhancers	HSMMtube	muscle

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