Variant report

Variant	rs6462060
Chromosome Location	chr7:27980319-27980320
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10951187	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11763181	1.00[CEU][hapmap]
rs12538288	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1557779	0.85[CEU][hapmap]
rs1859109	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs191	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs197	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs200	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs201	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs205	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs207	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs208	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2097737	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs211	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs213	0.85[CEU][hapmap]
rs215	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs218	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4722746	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6951040	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6955462	0.82[CEU][hapmap]
rs6958293	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6968362	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs6968677	1.00[CEU][hapmap]
rs6969949	0.85[CEU][hapmap]
rs6970113	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6972944	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73083394	0.85[EUR][1000 genomes]
rs7778340	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7783410	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7787507	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs916854	0.85[CEU][hapmap];0.89[AMR][1000 genomes];0.91[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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27941400-27990800	Weak transcription	Primary T cells from cord blood	blood
2	chr7:27942400-28005600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr7:27957600-28000800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr7:27961000-27983400	Weak transcription	NH-A	brain
5	chr7:27973600-27982600	Weak transcription	Spleen	Spleen
6	chr7:27973800-27986200	Weak transcription	HSMM	muscle
7	chr7:27974000-27980800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr7:27974000-27981200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr7:27974000-27981400	Weak transcription	Primary neutrophils fromperipheralblood	blood
10	chr7:27974000-27990800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr7:27975600-27981000	Weak transcription	Adipose Nuclei	Adipose
12	chr7:27975600-27984800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr7:27976200-27987400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr7:27976400-27981800	Weak transcription	Fetal Muscle Leg	muscle
15	chr7:27976600-27981800	Weak transcription	Fetal Lung	lung
16	chr7:27976600-27991600	Weak transcription	Osteobl	bone
17	chr7:27976800-27982200	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr7:27977000-27981000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr7:27977000-27983600	Weak transcription	Psoas Muscle	Psoas
20	chr7:27977000-27983600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr7:27977000-28001400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr7:27977200-27981000	Weak transcription	NHDF-Ad	bronchial
23	chr7:27977200-27986400	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr7:27977400-27981000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:27977400-27981000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr7:27977400-27991600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:27978600-27993000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr7:27979000-27980400	Enhancers	Fetal Heart	heart
29	chr7:27979000-27980400	ZNF genes & repeats	Fetal Stomach	stomach
30	chr7:27979000-27980600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr7:27979000-27981800	Enhancers	Colon Smooth Muscle	Colon
32	chr7:27979000-27984800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:27979200-27980400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr7:27979200-27980400	Enhancers	Left Ventricle	heart
35	chr7:27979200-27981200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:27979200-27982400	Weak transcription	Right Atrium	heart
37	chr7:27979200-27985600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr7:27979200-28000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr7:27979400-27981800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:27979600-27983000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr7:27979800-27980400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr7:27979800-27980400	ZNF genes & repeats	Aorta	Aorta
43	chr7:27979800-27980400	Flanking Active TSS	Brain Substantia Nigra	brain
44	chr7:27979800-27980600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr7:27980000-27980400	Active TSS	Brain Hippocampus Middle	brain
46	chr7:27980000-27980400	Enhancers	Fetal Brain Male	brain
47	chr7:27980000-27980400	ZNF genes & repeats	Pancreas	Pancrea
48	chr7:27980000-27980800	Weak transcription	Brain Angular Gyrus	brain
49	chr7:27980000-27981200	Weak transcription	Brain Anterior Caudate	brain
50	chr7:27980000-27982000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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