Variant report

Variant	rs557484
Chromosome Location	chr11:77089651-77089652
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:77080789..77082811-chr11:77088019..77090076,2	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs11237141	0.87[ASN][1000 genomes]
rs11237142	0.87[ASN][1000 genomes]
rs11237148	0.87[ASN][1000 genomes]
rs11237150	0.87[ASN][1000 genomes]
rs11237151	0.87[ASN][1000 genomes]
rs11237162	0.85[AMR][1000 genomes]
rs11237164	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1125619	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1225478	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12361757	0.87[ASN][1000 genomes]
rs12363707	0.87[ASN][1000 genomes]
rs12363842	0.87[ASN][1000 genomes]
rs12366261	0.84[ASN][1000 genomes]
rs1237490	0.88[EUR][1000 genomes]
rs12794253	0.87[ASN][1000 genomes]
rs1377472	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1597954	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1622364	0.87[ASN][1000 genomes]
rs1670446	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1670449	0.87[ASN][1000 genomes]
rs1670450	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1670456	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1670458	0.87[ASN][1000 genomes]
rs1670461	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1670462	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17824184	0.87[ASN][1000 genomes]
rs1793468	0.87[ASN][1000 genomes]
rs1793471	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1793472	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1793487	0.87[ASN][1000 genomes]
rs1793490	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2154754	0.82[EUR][1000 genomes]
rs2156567	0.87[ASN][1000 genomes]
rs2602476	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2602483	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2602487	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2725820	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2725822	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2725825	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2725828	0.92[ASN][1000 genomes]
rs3015982	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015983	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015985	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015986	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015988	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015990	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015992	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3019233	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3019234	0.95[EUR][1000 genomes]
rs3019235	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3019236	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3019249	0.87[EUR][1000 genomes]
rs3019257	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34025917	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34880271	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4375461	0.87[ASN][1000 genomes]
rs472691	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs476258	0.88[EUR][1000 genomes]
rs479104	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs493256	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs494289	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs503406	0.96[EUR][1000 genomes]
rs505841	0.89[EUR][1000 genomes]
rs508662	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs51500	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs520938	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs522015	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs523481	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs531638	0.86[EUR][1000 genomes]
rs535008	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs552323	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs558470	0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs560571	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs561386	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs562845	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs563731	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs572485	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs576220	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs580624	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs592602	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs595654	0.86[EUR][1000 genomes]
rs598801	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs644551	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs649040	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs653792	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs657269	0.82[EUR][1000 genomes]
rs66518011	0.84[ASN][1000 genomes]
rs66540426	0.87[ASN][1000 genomes]
rs66728428	0.87[ASN][1000 genomes]
rs674259	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs683455	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs683762	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs684793	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs686068	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs689108	0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7934230	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7949721	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs883680	0.87[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	nsv1048360	chr11:76900813-77387933	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv541089	chr11:76900813-77387933	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1049603	chr11:76900813-77520411	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv541090	chr11:76900813-77520411	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv3424135	chr11:76961603-77277087	Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1037724	chr11:77061945-77250391	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv541091	chr11:77061945-77250391	Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:77033400-77090400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr11:77046200-77092400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr11:77046800-77121600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:77047200-77096000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr11:77047400-77090000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:77055200-77092200	Weak transcription	Small Intestine	intestine
7	chr11:77055200-77117600	Weak transcription	Pancreas	Pancrea
8	chr11:77064200-77102800	Weak transcription	Brain Substantia Nigra	brain
9	chr11:77066800-77090000	Weak transcription	Brain Angular Gyrus	brain
10	chr11:77067000-77092800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr11:77067000-77093800	Weak transcription	Psoas Muscle	Psoas
12	chr11:77067000-77097000	Weak transcription	Esophagus	oesophagus
13	chr11:77067200-77111800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr11:77068800-77097000	Weak transcription	Brain Cingulate Gyrus	brain
15	chr11:77069000-77090000	Weak transcription	Fetal Lung	lung
16	chr11:77070000-77102000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr11:77075200-77097200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr11:77077000-77090000	Weak transcription	Fetal Thymus	thymus
19	chr11:77077200-77091800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:77077600-77092800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:77078000-77091600	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr11:77081000-77093400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr11:77081000-77094600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr11:77081200-77091000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:77081200-77091600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:77081200-77091800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr11:77081200-77095600	Strong transcription	GM12878-XiMat	blood
28	chr11:77081200-77096600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:77082000-77095600	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:77082000-77096200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr11:77082200-77091200	Strong transcription	Placenta	Placenta
32	chr11:77082200-77091400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr11:77082200-77091400	Strong transcription	Primary T cells from cord blood	blood
34	chr11:77082200-77092800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr11:77082200-77095800	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr11:77082400-77090600	Weak transcription	Right Ventricle	heart
37	chr11:77082400-77104200	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr11:77083000-77091000	Strong transcription	Duodenum Mucosa	Duodenum
39	chr11:77083200-77092000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:77083400-77091000	Strong transcription	Fetal Muscle Leg	muscle
41	chr11:77083400-77091600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr11:77084000-77093200	Weak transcription	Hela-S3	cervix
43	chr11:77084000-77111400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:77084200-77107000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr11:77084400-77091200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr11:77084400-77103600	Weak transcription	Fetal Kidney	kidney
47	chr11:77084600-77121200	Weak transcription	Thymus	Thymus
48	chr11:77085000-77090000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr11:77085600-77090200	Weak transcription	Fetal Brain Male	brain
50	chr11:77085600-77092800	Weak transcription	HSMMtube	muscle

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