Variant report

Variant	rs12365540
Chromosome Location	chr11:9917109-9917110
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10770072	0.98[ASN][1000 genomes]
rs10770074	0.91[ASN][1000 genomes]
rs10840316	0.91[AFR][1000 genomes]
rs12099354	0.87[EUR][1000 genomes]
rs12360818	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12365901	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12796169	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12800780	0.87[AFR][1000 genomes]
rs1546541	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1546542	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35396321	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4334006	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4445629	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4498988	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4616018	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4910073	0.91[AFR][1000 genomes]
rs4910076	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6483809	0.94[ASN][1000 genomes]
rs6483811	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67701335	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7105337	0.94[ASN][1000 genomes]
rs7107328	0.85[EUR][1000 genomes]
rs7126063	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7130923	0.91[ASN][1000 genomes]
rs7131516	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7350496	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7925651	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7929338	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7930281	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7948688	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7950655	0.82[ASN][1000 genomes]
rs9919605	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9919608	0.90[ASN][1000 genomes]
rs9919609	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9919617	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9919633	0.91[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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9878800-9952200	Weak transcription	Aorta	Aorta
2	chr11:9882400-9929600	Weak transcription	Primary T cells from cord blood	blood
3	chr11:9892400-9921200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr11:9894400-9978600	Weak transcription	Left Ventricle	heart
5	chr11:9902200-9917400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:9904000-9937000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr11:9906800-9920400	Weak transcription	HUVEC	blood vessel
8	chr11:9910000-9954600	Weak transcription	Pancreas	Pancrea
9	chr11:9910200-9921000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr11:9911600-9919200	Weak transcription	Fetal Brain Female	brain
11	chr11:9911800-9921200	Weak transcription	HMEC	breast
12	chr11:9913400-9919800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr11:9913400-9921000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:9913600-9921200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:9913600-9928800	Weak transcription	Right Ventricle	heart
16	chr11:9913800-9927400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:9914200-9926800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr11:9914400-9917400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:9914400-9917800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr11:9914400-9927600	Weak transcription	Brain Anterior Caudate	brain
21	chr11:9914600-9917400	Weak transcription	Dnd41	blood
22	chr11:9914600-9917600	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr11:9914800-9917400	Strong transcription	Placenta	Placenta
24	chr11:9914800-9917600	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr11:9915000-9917600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:9915000-9917600	Strong transcription	Liver	Liver
27	chr11:9915000-9918600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:9915000-9921000	Weak transcription	Hela-S3	cervix
29	chr11:9915000-9937200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:9915200-9917200	Strong transcription	Ovary	ovary
31	chr11:9915200-9917600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr11:9915200-9922600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr11:9915400-9921400	Weak transcription	NHLF	lung
34	chr11:9915400-9923200	Weak transcription	HSMMtube	muscle
35	chr11:9915400-9926800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr11:9915400-9927600	Weak transcription	Colon Smooth Muscle	Colon
37	chr11:9915600-9921200	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr11:9915600-9923400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr11:9915800-9923000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr11:9916200-9917200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
41	chr11:9916200-9917400	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr11:9916200-9917600	Enhancers	Muscle Satellite Cultured Cells	--
43	chr11:9916200-9917800	Enhancers	NHDF-Ad	bronchial
44	chr11:9916400-9917200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr11:9916400-9917200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
46	chr11:9916400-9917200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
47	chr11:9916400-9917600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:9916400-9917800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
49	chr11:9916400-9918400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr11:9916600-9917200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell

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