Variant report

Variant	rs16970707
Chromosome Location	chr16:72236679-72236680
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:72231856..72234002-chr16:72234236..72237028,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12447857	0.86[AFR][1000 genomes]
rs16970718	0.82[LWK][hapmap];0.81[YRI][hapmap]
rs16970725	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2189680	1.00[CEU][hapmap]
rs34417180	1.00[ASN][1000 genomes]
rs35549608	1.00[ASN][1000 genomes]
rs55771535	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58415520	0.81[AFR][1000 genomes]
rs60701149	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61452478	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6499566	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7187517	0.80[AFR][1000 genomes]
rs9302635	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9930957	1.00[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	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
3	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
4	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
5	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
6	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
8	nsv1059599	chr16:72219769-72342170	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1066473	chr16:72229094-72373598	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16970707	HP	cis	multi-tissue	Pritchard
rs16970707	HPR	cis	Whole Blood	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72229200-72240200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr16:72232400-72237000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr16:72233000-72237200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr16:72233000-72240400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr16:72233200-72240000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr16:72233800-72237000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr16:72234000-72237000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr16:72234200-72237600	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr16:72235000-72237000	Weak transcription	Brain Anterior Caudate	brain
10	chr16:72235400-72238000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr16:72235400-72238000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr16:72235800-72237800	Enhancers	Duodenum Mucosa	Duodenum
13	chr16:72235800-72237800	Enhancers	Fetal Intestine Large	intestine
14	chr16:72235800-72238000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr16:72235800-72238000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr16:72235800-72238000	Enhancers	Fetal Intestine Small	intestine
17	chr16:72235800-72238000	Enhancers	HMEC	breast
18	chr16:72236000-72236800	Enhancers	Placenta Amnion	Placenta Amnion
19	chr16:72236000-72236800	Active TSS	Rectal Mucosa Donor 31	rectum
20	chr16:72236000-72237400	Enhancers	NHDF-Ad	bronchial
21	chr16:72236000-72237600	Enhancers	Pancreas	Pancrea
22	chr16:72236000-72238000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr16:72236000-72240800	Weak transcription	Fetal Brain Male	brain
24	chr16:72236200-72237000	Enhancers	Fetal Brain Female	brain
25	chr16:72236200-72237200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr16:72236200-72238000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr16:72236200-72238000	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr16:72236400-72237000	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr16:72236400-72237800	Enhancers	Fetal Lung	lung
30	chr16:72236400-72238000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr16:72236400-72238000	Enhancers	Stomach Mucosa	stomach
32	chr16:72236400-72238400	Enhancers	Primary B cells from peripheral blood	blood
33	chr16:72236600-72236800	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr16:72236600-72237000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr16:72236600-72237000	Flanking Active TSS	Primary hematopoietic stem cells	blood
36	chr16:72236600-72237000	Flanking Active TSS	NHEK	skin
37	chr16:72236600-72237200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr16:72236600-72237200	Enhancers	HUVEC	blood vessel
39	chr16:72236600-72237400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr16:72236600-72237400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr16:72236600-72237800	Flanking Active TSS	Primary B cells from cord blood	blood
42	chr16:72236600-72237800	Enhancers	Brain Hippocampus Middle	brain
43	chr16:72236600-72238000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr16:72236600-72238000	Enhancers	Esophagus	oesophagus
45	chr16:72236600-72244000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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