Variant report

Variant	rs561153
Chromosome Location	chr11:77090037-77090038
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	chr11:77080789..77082811-chr11:77088019..77090076,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10793248	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11607378	0.84[EUR][1000 genomes]
rs1225479	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2007466	0.82[EUR][1000 genomes]
rs2602463	0.83[ASN][1000 genomes]
rs2725812	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2729747	0.83[ASN][1000 genomes]
rs2729753	0.84[ASN][1000 genomes]
rs2729771	0.83[ASN][1000 genomes]
rs2853097	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015984	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3015989	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015991	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3015993	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3019240	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3019243	0.83[EUR][1000 genomes]
rs3019258	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34420077	0.84[EUR][1000 genomes]
rs4433591	0.85[EUR][1000 genomes]
rs473012	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs476258	0.80[AFR][1000 genomes]
rs476925	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs478134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478475	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs482243	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs487322	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs489038	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs491781	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs492527	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4944153	0.81[EUR][1000 genomes]
rs4944155	0.84[EUR][1000 genomes]
rs4944158	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4945162	0.83[EUR][1000 genomes]
rs4945166	0.84[EUR][1000 genomes]
rs4945169	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs495889	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs497172	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs499880	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs500731	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs514191	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs517511	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs538670	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs539906	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs556696	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs562939	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs568309	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57129983	0.84[EUR][1000 genomes]
rs575662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs576079	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs576997	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs584909	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs599437	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs605910	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs614775	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs618012	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61901769	0.83[EUR][1000 genomes]
rs61901771	0.81[EUR][1000 genomes]
rs61901802	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs628325	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs635291	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs639857	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6592714	0.81[EUR][1000 genomes]
rs6592715	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs667331	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs683497	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs688212	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7118869	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs721382	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs73496890	0.85[EUR][1000 genomes]
rs7928731	0.84[EUR][1000 genomes]
rs98703	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[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	chr11:77055200-77092200	Weak transcription	Small Intestine	intestine
6	chr11:77055200-77117600	Weak transcription	Pancreas	Pancrea
7	chr11:77064200-77102800	Weak transcription	Brain Substantia Nigra	brain
8	chr11:77067000-77092800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:77067000-77093800	Weak transcription	Psoas Muscle	Psoas
10	chr11:77067000-77097000	Weak transcription	Esophagus	oesophagus
11	chr11:77067200-77111800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:77068800-77097000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:77070000-77102000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr11:77075200-77097200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr11:77077200-77091800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr11:77077600-77092800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr11:77078000-77091600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr11:77081000-77093400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:77081000-77094600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr11:77081200-77091000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:77081200-77091600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr11:77081200-77091800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr11:77081200-77095600	Strong transcription	GM12878-XiMat	blood
24	chr11:77081200-77096600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:77082000-77095600	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr11:77082000-77096200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:77082200-77091200	Strong transcription	Placenta	Placenta
28	chr11:77082200-77091400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
29	chr11:77082200-77091400	Strong transcription	Primary T cells from cord blood	blood
30	chr11:77082200-77092800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr11:77082200-77095800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr11:77082400-77090600	Weak transcription	Right Ventricle	heart
33	chr11:77082400-77104200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr11:77083000-77091000	Strong transcription	Duodenum Mucosa	Duodenum
35	chr11:77083200-77092000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:77083400-77091000	Strong transcription	Fetal Muscle Leg	muscle
37	chr11:77083400-77091600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:77084000-77093200	Weak transcription	Hela-S3	cervix
39	chr11:77084000-77111400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:77084200-77107000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr11:77084400-77091200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr11:77084400-77103600	Weak transcription	Fetal Kidney	kidney
43	chr11:77084600-77121200	Weak transcription	Thymus	Thymus
44	chr11:77085600-77090200	Weak transcription	Fetal Brain Male	brain
45	chr11:77085600-77092800	Weak transcription	HSMMtube	muscle
46	chr11:77086400-77090200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr11:77086400-77093400	Weak transcription	Stomach Mucosa	stomach
48	chr11:77086400-77108000	Weak transcription	Brain Anterior Caudate	brain
49	chr11:77086600-77090200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr11:77086600-77090800	Weak transcription	A549	lung

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