Variant report

Variant	rs11654553
Chromosome Location	chr17:17462149-17462150
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17460442..17462170-chr17:17466315..17469039,2	MCF-7	breast:
2	chr17:17460513..17462662-chr17:17475967..17478047,2	MCF-7	breast:
3	chr17:17453470..17455947-chr17:17461271..17462864,2	MCF-7	breast:
4	chr17:17447568..17449636-chr17:17462055..17463779,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10401038	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11651280	0.90[EUR][1000 genomes]
rs11654777	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11658311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13342397	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16961845	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28583584	0.89[EUR][1000 genomes]
rs28636952	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28652618	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35301480	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35838363	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56030759	0.87[EUR][1000 genomes]
rs58729290	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60831194	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7210978	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7214152	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7214988	0.89[EUR][1000 genomes]
rs7215055	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7216223	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7222358	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7224725	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7225421	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73978969	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8064558	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8070432	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8074742	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8081961	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9889584	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9889795	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9890062	0.82[AMR][1000 genomes]
rs9897362	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9903468	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9903503	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9904004	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9905032	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9905191	1.00[EUR][1000 genomes]
rs9910747	1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9944423	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907731	chr17:17358004-17504856	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv907736	chr17:17381764-17465458	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv907744	chr17:17404586-17504856	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv907746	chr17:17412032-17478917	Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv907747	chr17:17412032-17504856	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
7	nsv470579	chr17:17424332-17493810	Genic enhancers Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
9	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv1062052	chr17:17461050-17507199	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv543237	chr17:17461050-17507199	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17418200-17478000	Weak transcription	Primary T cells from cord blood	blood
2	chr17:17436800-17479200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr17:17443400-17467000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr17:17444200-17467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr17:17444400-17469200	Weak transcription	Fetal Brain Female	brain
6	chr17:17444600-17464600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr17:17444800-17464000	Weak transcription	Esophagus	oesophagus
8	chr17:17445200-17468400	Weak transcription	Thymus	Thymus
9	chr17:17445200-17473200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr17:17449000-17464800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr17:17449600-17464800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr17:17449600-17467000	Weak transcription	Ovary	ovary
13	chr17:17450800-17467800	Weak transcription	Brain Germinal Matrix	brain
14	chr17:17451000-17468400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr17:17453200-17468200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr17:17453400-17477800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr17:17454800-17469800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr17:17455000-17462600	Weak transcription	Gastric	stomach
19	chr17:17455000-17468600	Weak transcription	Brain Substantia Nigra	brain
20	chr17:17455200-17463200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr17:17455200-17466400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr17:17455200-17466800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr17:17455200-17468000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr17:17455200-17468000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr17:17455200-17469200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr17:17455200-17471800	Weak transcription	HepG2	liver
27	chr17:17456200-17468000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr17:17456800-17464600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr17:17456800-17464800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr17:17457800-17465200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr17:17459400-17462400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr17:17459600-17464200	Weak transcription	Lung	lung
33	chr17:17459800-17465000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr17:17460600-17464800	Weak transcription	Fetal Muscle Leg	muscle
35	chr17:17460600-17469200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr17:17460800-17462200	Enhancers	Adipose Nuclei	Adipose
37	chr17:17461000-17474000	Enhancers	Liver	Liver
38	chr17:17461200-17464400	Weak transcription	Spleen	Spleen
39	chr17:17461200-17464600	Weak transcription	Fetal Stomach	stomach
40	chr17:17461200-17465000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr17:17461200-17465400	Weak transcription	Brain Anterior Caudate	brain
42	chr17:17461200-17468400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr17:17461400-17463200	Weak transcription	Psoas Muscle	Psoas
44	chr17:17461400-17463400	Weak transcription	Stomach Mucosa	stomach
45	chr17:17461400-17464000	Weak transcription	Right Ventricle	heart
46	chr17:17461400-17465000	Weak transcription	Pancreas	Pancrea
47	chr17:17461400-17465000	Weak transcription	Right Atrium	heart
48	chr17:17461600-17462600	Weak transcription	Left Ventricle	heart
49	chr17:17461600-17464600	Weak transcription	Fetal Intestine Small	intestine
50	chr17:17461600-17465200	Weak transcription	Brain Hippocampus Middle	brain

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