Variant report

Variant	rs35406616
Chromosome Location	chr17:15417042-15417043
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	chr17:15411701..15413782-chr17:15416873..15418569,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10153259	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12450262	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450302	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12450921	0.85[ASN][1000 genomes]
rs12451284	0.82[ASN][1000 genomes]
rs12452965	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12453059	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12453117	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12938444	1.00[ASN][1000 genomes]
rs12939314	0.83[ASN][1000 genomes]
rs12943480	0.85[ASN][1000 genomes]
rs12948266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12953212	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17702522	1.00[ASN][1000 genomes]
rs17702771	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17775544	0.83[AMR][1000 genomes]
rs2013835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34236889	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34358805	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34453320	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34818581	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs35078459	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs35448233	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35699886	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36097878	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3852809	0.83[ASN][1000 genomes]
rs3911955	0.83[ASN][1000 genomes]
rs4791625	0.83[ASN][1000 genomes]
rs4792619	0.87[ASN][1000 genomes]
rs6502459	0.83[ASN][1000 genomes]
rs67294543	0.86[ASN][1000 genomes]
rs71367505	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71367507	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs716388	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7359511	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8068610	0.85[ASN][1000 genomes]
rs8070714	0.85[ASN][1000 genomes]
rs8071082	0.85[ASN][1000 genomes]
rs917567	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492304	chr17:15043353-15611753	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv916652	chr17:15093600-15856310	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv427990	chr17:15154329-15434020	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1055677	chr17:15294011-15561130	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv1059056	chr17:15294011-15856861	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
6	nsv1058286	chr17:15315763-15561130	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv543213	chr17:15315763-15561130	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:15383200-15419600	Weak transcription	Thymus	Thymus
2	chr17:15383400-15455000	Weak transcription	Gastric	stomach
3	chr17:15385600-15418000	Weak transcription	Pancreas	Pancrea
4	chr17:15393400-15451200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr17:15394800-15450800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr17:15396000-15417200	Weak transcription	Fetal Brain Male	brain
7	chr17:15396800-15420400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr17:15401200-15420400	Weak transcription	Psoas Muscle	Psoas
9	chr17:15405400-15418200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr17:15405400-15419000	Weak transcription	Liver	Liver
11	chr17:15406200-15420600	Weak transcription	Colonic Mucosa	Colon
12	chr17:15406600-15417200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:15406600-15419000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr17:15406600-15419800	Weak transcription	NHEK	skin
15	chr17:15406600-15422800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr17:15406600-15428800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr17:15406800-15418200	Weak transcription	Placenta	Placenta
18	chr17:15406800-15418600	Weak transcription	Spleen	Spleen
19	chr17:15406800-15419000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr17:15406800-15419200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr17:15406800-15419400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr17:15406800-15419400	Weak transcription	Fetal Kidney	kidney
23	chr17:15406800-15419600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr17:15406800-15420200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr17:15406800-15421800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr17:15406800-15422000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr17:15406800-15450600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr17:15407000-15419000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr17:15407000-15422400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr17:15410200-15426200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr17:15410800-15417200	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr17:15410800-15417400	Weak transcription	Primary T cells from cord blood	blood
33	chr17:15410800-15418200	Weak transcription	Fetal Brain Female	brain
34	chr17:15410800-15418600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr17:15410800-15418600	Weak transcription	Brain Germinal Matrix	brain
36	chr17:15410800-15429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:15412000-15417200	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr17:15412000-15417200	Weak transcription	Aorta	Aorta
39	chr17:15412000-15418000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr17:15412000-15418200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr17:15413000-15419200	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr17:15413200-15418000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr17:15413200-15418200	Weak transcription	Fetal Intestine Small	intestine
44	chr17:15413200-15419400	Weak transcription	Lung	lung
45	chr17:15413200-15420000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr17:15413400-15417200	Weak transcription	Fetal Intestine Large	intestine
47	chr17:15413400-15417600	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr17:15413600-15417600	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr17:15413800-15418800	Weak transcription	Adipose Nuclei	Adipose
50	chr17:15413800-15428000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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