Variant report

Variant	rs38499
Chromosome Location	chr7:28012458-28012459
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1023520	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10248014	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2106923	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs38501	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs38505	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs38506	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs38508	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs38512	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs38520	0.87[AMR][1000 genomes]
rs4722749	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6462062	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6955462	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6974886	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs957763	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs957764	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs995367	1.00[AMR][1000 genomes];0.98[EUR][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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1024819	chr7:27949955-28020969	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27980400-28017200	Weak transcription	Aorta	Aorta
2	chr7:27992000-28013400	Weak transcription	Left Ventricle	heart
3	chr7:27998400-28015000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr7:28000600-28019400	Weak transcription	Pancreas	Pancrea
5	chr7:28000600-28021600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:28001000-28013400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr7:28002600-28016800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr7:28002800-28034600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr7:28006200-28012800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:28006200-28015600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr7:28006200-28019200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr7:28006200-28024800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:28006400-28013400	Weak transcription	Brain Cingulate Gyrus	brain
14	chr7:28006400-28031800	Weak transcription	NHDF-Ad	bronchial
15	chr7:28006600-28016000	Weak transcription	Colon Smooth Muscle	Colon
16	chr7:28007000-28019200	Weak transcription	Esophagus	oesophagus
17	chr7:28008200-28013400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:28009800-28021600	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr7:28011200-28013000	Weak transcription	Brain Angular Gyrus	brain
20	chr7:28011400-28013400	Weak transcription	Brain Anterior Caudate	brain
21	chr7:28011600-28013000	Weak transcription	Brain Substantia Nigra	brain
22	chr7:28011800-28012600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr7:28011800-28013400	Weak transcription	Primary B cells from cord blood	blood
24	chr7:28011800-28014200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr7:28012000-28013400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr7:28012200-28012800	Enhancers	Dnd41	blood
27	chr7:28012200-28013400	Weak transcription	Brain Hippocampus Middle	brain
28	chr7:28012200-28013600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr7:28012200-28014000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr7:28012200-28014800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr7:28012400-28012600	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr7:28012400-28012800	Weak transcription	Fetal Thymus	thymus
33	chr7:28012400-28013400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr7:28012400-28013400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr7:28012400-28013600	Enhancers	Primary T cells from cord blood	blood
36	chr7:28012400-28013600	Enhancers	Primary T cells fromperipheralblood	blood
37	chr7:28012400-28013600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr7:28012400-28013600	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr7:28012400-28013800	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr7:28012400-28014000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr7:28012400-28014800	Weak transcription	Thymus	Thymus
42	chr7:28012400-28022200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr7:28012400-28028000	Weak transcription	Primary B cells from peripheral blood	blood

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