Variant report

Variant	rs11890286
Chromosome Location	chr2:11836699-11836700
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs28584687	0.89[ASN][1000 genomes]
rs4233903	0.83[EUR][1000 genomes]
rs55676775	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56858654	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57456819	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58273936	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58454451	0.94[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59502453	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59838011	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61410870	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61430487	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6432234	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67334974	0.89[ASN][1000 genomes]
rs6754255	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6757729	0.83[EUR][1000 genomes]
rs73177496	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179361	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179363	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179396	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73179398	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73181372	0.81[EUR][1000 genomes]
rs73181378	0.91[EUR][1000 genomes]
rs7556803	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580386	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7580501	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581186	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581192	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583977	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7583991	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594198	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7594406	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597552	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597790	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598525	1.00[ASN][1000 genomes]
rs7601181	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606137	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606378	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7606724	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv1003899	chr2:11789374-12248081	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
4	nsv469449	chr2:11808654-11854012	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv580972	chr2:11808654-11854012	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	esv10240	chr2:11832427-11837975	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11828800-11836800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:11829000-11836800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:11829200-11836800	Weak transcription	HUVEC	blood vessel
4	chr2:11829200-11837000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr2:11829200-11837000	Weak transcription	HSMM	muscle
6	chr2:11829200-11838400	Weak transcription	Fetal Lung	lung
7	chr2:11829400-11836800	Weak transcription	Brain Substantia Nigra	brain
8	chr2:11829400-11836800	Weak transcription	Colon Smooth Muscle	Colon
9	chr2:11829400-11837000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:11829400-11837000	Weak transcription	Fetal Heart	heart
11	chr2:11829400-11841800	Weak transcription	Primary B cells from cord blood	blood
12	chr2:11833600-11836800	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr2:11833600-11836800	Weak transcription	Placenta	Placenta
14	chr2:11833600-11836800	Weak transcription	Gastric	stomach
15	chr2:11833600-11836800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:11833600-11836800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr2:11833600-11836800	Weak transcription	Hela-S3	cervix
18	chr2:11833600-11837000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr2:11833600-11837000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:11833600-11838000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:11833600-11841800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:11833800-11836800	Weak transcription	Adipose Nuclei	Adipose
23	chr2:11833800-11836800	Weak transcription	Pancreas	Pancrea
24	chr2:11833800-11837000	Weak transcription	Colonic Mucosa	Colon
25	chr2:11833800-11837400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr2:11833800-11838000	Weak transcription	Liver	Liver
27	chr2:11833800-11838000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr2:11835200-11837600	Enhancers	Psoas Muscle	Psoas
29	chr2:11835400-11839200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:11836000-11839000	Enhancers	Primary hematopoietic stem cells	blood
31	chr2:11836400-11836800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:11836400-11836800	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr2:11836400-11837000	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr2:11836400-11839000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:11836600-11837200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr2:11836600-11837200	Enhancers	Brain Hippocampus Middle	brain
37	chr2:11836600-11837400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:11836600-11837400	Enhancers	Brain Anterior Caudate	brain
39	chr2:11836600-11837800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr2:11836600-11837800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
41	chr2:11836600-11838000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:11836600-11838000	Genic enhancers	Right Atrium	heart
43	chr2:11836600-11838200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr2:11836600-11838200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr2:11836600-11838200	Enhancers	Ovary	ovary
46	chr2:11836600-11838200	Enhancers	HMEC	breast
47	chr2:11836600-11838400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:11836600-11838400	Bivalent Enhancer	Fetal Stomach	stomach
49	chr2:11836600-11838400	Enhancers	Fetal Thymus	thymus
50	chr2:11836600-11838600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links