Variant report

Variant	rs11654842
Chromosome Location	chr17:17462620-17462621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17460513..17462662-chr17:17475967..17478047,2	MCF-7	breast:
2	chr17:17453470..17455947-chr17:17461271..17462864,2	MCF-7	breast:
3	chr17:17462313..17464083-chr17:17498964..17501075,2	K562	blood:
4	chr17:17447568..17449636-chr17:17462055..17463779,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11078389	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11651620	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12941371	0.86[ASN][1000 genomes]
rs12948060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1531100	0.95[CEU][hapmap]
rs2124344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3760188	0.82[CEU][hapmap]
rs4244596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4244598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646340	0.86[CEU][hapmap]
rs4646341	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs4646343	0.82[CEU][hapmap]
rs4646344	0.82[CEU][hapmap]
rs4646346	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4646347	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4646349	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4646350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646351	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646356	0.95[CEU][hapmap]
rs4646357	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646359	0.95[CEU][hapmap]
rs4646365	0.95[CEU][hapmap]
rs4646369	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4646370	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646371	0.82[CEU][hapmap]
rs4646372	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4646387	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4646389	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs4646390	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4646391	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4646392	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4646394	0.94[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4646395	0.90[ASN][1000 genomes]
rs6502603	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7209113	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7221487	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs729974	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs729975	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs747770	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs750546	0.86[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs8079427	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8080165	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8082417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs897451	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9892560	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9893179	0.90[ASN][1000 genomes]
rs9894321	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9894588	0.84[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	chr17:17455000-17468600	Weak transcription	Brain Substantia Nigra	brain
19	chr17:17455200-17463200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:17455200-17466400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr17:17455200-17466800	Weak transcription	Duodenum Mucosa	Duodenum
22	chr17:17455200-17468000	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr17:17455200-17468000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr17:17455200-17469200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr17:17455200-17471800	Weak transcription	HepG2	liver
26	chr17:17456200-17468000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr17:17456800-17464600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr17:17456800-17464800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr17:17457800-17465200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr17:17459600-17464200	Weak transcription	Lung	lung
31	chr17:17459800-17465000	Weak transcription	Primary B cells from peripheral blood	blood
32	chr17:17460600-17464800	Weak transcription	Fetal Muscle Leg	muscle
33	chr17:17460600-17469200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr17:17461000-17474000	Enhancers	Liver	Liver
35	chr17:17461200-17464400	Weak transcription	Spleen	Spleen
36	chr17:17461200-17464600	Weak transcription	Fetal Stomach	stomach
37	chr17:17461200-17465000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr17:17461200-17465400	Weak transcription	Brain Anterior Caudate	brain
39	chr17:17461200-17468400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr17:17461400-17463200	Weak transcription	Psoas Muscle	Psoas
41	chr17:17461400-17463400	Weak transcription	Stomach Mucosa	stomach
42	chr17:17461400-17464000	Weak transcription	Right Ventricle	heart
43	chr17:17461400-17465000	Weak transcription	Pancreas	Pancrea
44	chr17:17461400-17465000	Weak transcription	Right Atrium	heart
45	chr17:17461600-17464600	Weak transcription	Fetal Intestine Small	intestine
46	chr17:17461600-17465200	Weak transcription	Brain Hippocampus Middle	brain
47	chr17:17461600-17465400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr17:17461600-17468600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr17:17462000-17462800	Enhancers	Fetal Heart	heart
50	chr17:17462000-17464600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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