Variant report

Variant	rs17236648
Chromosome Location	chr3:160519845-160519846
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160513259..160516252-chr3:160518883..160520924,2	MCF-7	breast:
2	chr3:160518067..160520836-chr3:160522097..160523990,2	MCF-7	breast:
3	chr3:160511490..160513130-chr3:160518660..160520550,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1378662	0.85[AFR][1000 genomes]
rs1378663	0.90[AFR][1000 genomes]
rs1455870	0.94[EUR][1000 genomes]
rs1455871	0.94[EUR][1000 genomes]
rs16831442	0.94[EUR][1000 genomes]
rs16831457	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16831471	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831473	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16831516	0.94[EUR][1000 genomes]
rs16831520	0.94[EUR][1000 genomes]
rs17236620	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17236641	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17236655	1.00[EUR][1000 genomes]
rs17236662	0.94[EUR][1000 genomes]
rs17826352	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17826358	0.94[EUR][1000 genomes]
rs17826364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17826370	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17826376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068817	0.94[EUR][1000 genomes]
rs34035435	0.97[EUR][1000 genomes]
rs3907061	0.94[EUR][1000 genomes]
rs4549318	0.97[EUR][1000 genomes]
rs4627794	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55891037	1.00[EUR][1000 genomes]
rs55905728	1.00[EUR][1000 genomes]
rs55923270	0.94[EUR][1000 genomes]
rs55997050	1.00[EUR][1000 genomes]
rs56083575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56141155	1.00[EUR][1000 genomes]
rs56157815	1.00[EUR][1000 genomes]
rs56180903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56331465	1.00[EUR][1000 genomes]
rs57828617	0.94[EUR][1000 genomes]
rs58891820	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6771910	0.94[EUR][1000 genomes]
rs6779461	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73877952	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73877966	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618082	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618596	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629154	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633401	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160498400-160522600	Weak transcription	Right Ventricle	heart
2	chr3:160509000-160522600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr3:160513400-160522600	Weak transcription	Pancreas	Pancrea
4	chr3:160514200-160520000	Weak transcription	Left Ventricle	heart
5	chr3:160514400-160522600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:160515400-160526400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:160518400-160520400	Enhancers	Fetal Heart	heart
8	chr3:160518800-160520200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr3:160518800-160520400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr3:160518800-160522800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr3:160519000-160520000	Enhancers	Primary B cells from peripheral blood	blood
12	chr3:160519000-160520000	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr3:160519000-160520000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:160519000-160520000	Enhancers	Fetal Thymus	thymus
15	chr3:160519000-160520000	Active TSS	Psoas Muscle	Psoas
16	chr3:160519000-160520200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:160519000-160520200	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr3:160519000-160520200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr3:160519000-160520200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr3:160519000-160520200	Enhancers	Liver	Liver
21	chr3:160519000-160520200	Enhancers	Brain Angular Gyrus	brain
22	chr3:160519000-160520200	Enhancers	Brain Inferior Temporal Lobe	brain
23	chr3:160519000-160520200	Enhancers	Stomach Mucosa	stomach
24	chr3:160519000-160520400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr3:160519000-160521000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:160519200-160520000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:160519200-160520000	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr3:160519200-160520000	Active TSS	Right Atrium	heart
29	chr3:160519200-160520200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:160519200-160520200	Enhancers	Aorta	Aorta
31	chr3:160519200-160520200	Enhancers	Fetal Brain Female	brain
32	chr3:160519200-160520400	Enhancers	Primary T cells fromperipheralblood	blood
33	chr3:160519200-160520400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr3:160519200-160520400	Enhancers	Colonic Mucosa	Colon
35	chr3:160519200-160520400	Enhancers	Placenta	Placenta
36	chr3:160519200-160520400	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr3:160519200-160521000	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:160519200-160521000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr3:160519200-160521000	Enhancers	Sigmoid Colon	Sigmoid Colon
40	chr3:160519400-160520000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:160519400-160520000	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr3:160519400-160520000	Active TSS	Brain Cingulate Gyrus	brain
43	chr3:160519400-160520000	Bivalent Enhancer	Osteobl	bone
44	chr3:160519400-160520200	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr3:160519400-160520200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr3:160519400-160520200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:160519400-160520200	Flanking Active TSS	GM12878-XiMat	blood
48	chr3:160519600-160520000	Active TSS	Brain Hippocampus Middle	brain
49	chr3:160519600-160520200	Active TSS	Duodenum Mucosa	Duodenum
50	chr3:160519600-160520200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum

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