Variant report

Variant	rs11684088
Chromosome Location	chr2:100264583-100264584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10167554	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11123790	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12620982	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12712049	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12712054	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13029690	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1357719	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1996984	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2030691	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2030692	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2030693	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2049400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2177541	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2177542	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3792129	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3792130	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3792131	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4850910	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4851220	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4851221	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6542884	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6738724	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6745568	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579222	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9284724	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9308826	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9308827	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9678859	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003343	chr2:100241560-100848900	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv535843	chr2:100241560-100848900	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100253200-100308800	Weak transcription	Gastric	stomach
2	chr2:100254000-100265000	Weak transcription	Spleen	Spleen
3	chr2:100255400-100268600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:100255400-100285400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr2:100255400-100285400	Weak transcription	Dnd41	blood
6	chr2:100256600-100267400	Weak transcription	Fetal Thymus	thymus
7	chr2:100257600-100265000	Weak transcription	Left Ventricle	heart
8	chr2:100257600-100308600	Weak transcription	Thymus	Thymus
9	chr2:100259400-100274600	Weak transcription	Primary T cells from cord blood	blood
10	chr2:100260200-100283600	Strong transcription	Primary B cells from peripheral blood	blood
11	chr2:100260600-100265000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr2:100260800-100274400	Weak transcription	Right Atrium	heart
13	chr2:100261200-100264600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:100261200-100265000	Weak transcription	Brain Anterior Caudate	brain
15	chr2:100261400-100264600	Weak transcription	Brain Angular Gyrus	brain
16	chr2:100261400-100264600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:100261400-100264800	Weak transcription	Colon Smooth Muscle	Colon
18	chr2:100261400-100264800	Weak transcription	Fetal Muscle Leg	muscle
19	chr2:100261400-100264800	Weak transcription	Fetal Stomach	stomach
20	chr2:100261400-100264800	Weak transcription	Pancreas	Pancrea
21	chr2:100261400-100265000	Weak transcription	Brain Germinal Matrix	brain
22	chr2:100261400-100265000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:100261400-100265000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr2:100261400-100266800	Enhancers	Fetal Brain Male	brain
25	chr2:100261400-100268400	Weak transcription	NH-A	brain
26	chr2:100261400-100279000	Weak transcription	Fetal Kidney	kidney
27	chr2:100261600-100265000	Weak transcription	Adipose Nuclei	Adipose
28	chr2:100261600-100265000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:100261800-100265000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:100262400-100266800	Strong transcription	Primary B cells from cord blood	blood
31	chr2:100262800-100264800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:100263200-100264800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr2:100263800-100265000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:100263800-100266600	Enhancers	Fetal Lung	lung
35	chr2:100264000-100265000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:100264000-100266600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:100264000-100328600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr2:100264200-100264800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:100264200-100265800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:100264200-100266200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:100264200-100266200	Enhancers	Fetal Heart	heart
42	chr2:100264200-100266400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:100264200-100266400	Enhancers	Fetal Brain Female	brain
44	chr2:100264200-100281800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:100264400-100264800	Weak transcription	Ovary	ovary
46	chr2:100264400-100265800	Enhancers	NHDF-Ad	bronchial
47	chr2:100264400-100266000	Enhancers	Osteobl	bone
48	chr2:100264400-100266400	Enhancers	Cortex derived primary cultured neurospheres	brain

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