Variant report

Variant	rs454538
Chromosome Location	chr11:16868744-16868745
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:16868421..16871195-chr11:16872286..16874051,3	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1638456	0.85[AMR][1000 genomes]
rs1638457	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2057788	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs369457	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs370053	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs370671	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs371905	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs373266	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs376641	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs378863	0.88[AMR][1000 genomes]
rs379051	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs380655	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs382280	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs385627	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs385943	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs387849	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs389967	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs390974	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs391332	0.85[AMR][1000 genomes]
rs392706	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs393633	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs397343	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs397373	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs398216	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs400085	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs400349	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs400458	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs401820	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs402982	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs404492	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs406109	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs406890	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs406937	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs407354	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs407932	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs409354	0.98[AMR][1000 genomes]
rs415265	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs417349	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs417406	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs418034	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs420975	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs425325	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs425745	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs426085	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs427429	0.80[AMR][1000 genomes]
rs428933	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs429368	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs430211	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs431208	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs432046	0.85[AMR][1000 genomes]
rs432656	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs433212	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs433225	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs434761	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs434899	0.83[AMR][1000 genomes]
rs435206	0.80[AMR][1000 genomes]
rs439224	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs440212	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs443327	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs445146	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs445205	0.88[AMR][1000 genomes]
rs446518	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs446612	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs450828	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs452414	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs452745	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs453015	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs454869	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58555284	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7951328	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16813200-16871400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr11:16823000-16871400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:16839200-16878800	Weak transcription	Thymus	Thymus
4	chr11:16842600-16873400	Weak transcription	Hela-S3	cervix
5	chr11:16843000-16874600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:16846600-16874000	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr11:16847000-16871200	Weak transcription	Brain Substantia Nigra	brain
8	chr11:16847200-16871400	Weak transcription	Brain Hippocampus Middle	brain
9	chr11:16847800-16871600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr11:16848200-16871400	Weak transcription	Aorta	Aorta
11	chr11:16848200-16875200	Weak transcription	Right Ventricle	heart
12	chr11:16848400-16878600	Weak transcription	Small Intestine	intestine
13	chr11:16849800-16871400	Weak transcription	Pancreas	Pancrea
14	chr11:16850400-16871200	Weak transcription	Fetal Brain Female	brain
15	chr11:16850600-16871800	Weak transcription	Colonic Mucosa	Colon
16	chr11:16850800-16870600	Weak transcription	Fetal Brain Male	brain
17	chr11:16853400-16883800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:16855200-16873000	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr11:16855200-16877600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr11:16855200-16878800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr11:16858000-16876800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr11:16858200-16871600	Weak transcription	A549	lung
23	chr11:16858200-16878800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr11:16858400-16876400	Weak transcription	Brain Germinal Matrix	brain
25	chr11:16859200-16868800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:16860000-16870000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr11:16861200-16879800	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr11:16861800-16877000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:16861800-16880600	Weak transcription	HMEC	breast
30	chr11:16862200-16871800	Weak transcription	HSMM	muscle
31	chr11:16862200-16875200	Genic enhancers	Fetal Heart	heart
32	chr11:16862200-16876800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr11:16863200-16869800	Weak transcription	Brain Anterior Caudate	brain
34	chr11:16863200-16871800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr11:16863400-16870200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr11:16863400-16870800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr11:16863400-16875600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:16863400-16875600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:16863400-16882000	Weak transcription	Stomach Mucosa	stomach
40	chr11:16863800-16871400	Weak transcription	Gastric	stomach
41	chr11:16863800-16871600	Weak transcription	Placenta	Placenta
42	chr11:16863800-16875800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr11:16863800-16884800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr11:16863800-16892600	Weak transcription	Fetal Kidney	kidney
45	chr11:16864000-16871000	Weak transcription	Ovary	ovary
46	chr11:16864000-16871400	Weak transcription	Fetal Stomach	stomach
47	chr11:16864000-16871400	Weak transcription	Lung	lung
48	chr11:16864000-16871400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr11:16864000-16872200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr11:16864000-16878800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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