Variant report

Variant	rs62054710
Chromosome Location	chr16:31771949-31771950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:31768318..31770553-chr16:31771376..31773000,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10871458	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11150638	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1156903	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12716999	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12717000	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1406177	0.82[ASN][1000 genomes]
rs1528319	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs1881316	0.82[ASN][1000 genomes]
rs1919042	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2078924	0.81[EUR][1000 genomes]
rs2106579	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2106581	0.82[ASN][1000 genomes]
rs2157970	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2188619	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2359219	0.80[EUR][1000 genomes]
rs2359222	0.82[AMR][1000 genomes]
rs2359226	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2359455	0.85[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs28427454	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4620975	0.81[EUR][1000 genomes]
rs4889553	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4889555	0.80[ASN][1000 genomes]
rs4889688	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4889693	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62054709	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6565269	0.81[ASN][1000 genomes]
rs6565275	0.89[AMR][1000 genomes]
rs6565278	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6565280	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6565282	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6565285	0.80[EUR][1000 genomes]
rs6565286	0.83[ASN][1000 genomes]
rs6565287	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67922432	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7188627	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7190730	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs727349	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8049323	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8053712	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8060086	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8062424	0.81[ASN][1000 genomes]
rs8062902	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs916753	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs929208	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9921898	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9929892	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9930700	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9936002	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9938037	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
2	esv3344221	chr16:31526786-31821640	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	esv3323903	chr16:31526802-31821640	Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv3504445	chr16:31526873-31821580	Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
5	esv3504446	chr16:31526873-31821580	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	esv3366795	chr16:31534951-31827424	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1067321	chr16:31652036-31959992	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
8	nsv918074	chr16:31669781-31935033	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
9	nsv1063037	chr16:31669981-31934894	Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
10	nsv542903	chr16:31669981-31934894	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv905761	chr16:31730525-31812442	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	esv3446880	chr16:31734687-31891223	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31759800-31772600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
2	chr16:31759800-31788600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr16:31764200-31772200	Weak transcription	Pancreas	Pancrea
4	chr16:31766800-31774600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr16:31768800-31772200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr16:31768800-31775000	Weak transcription	Thymus	Thymus
7	chr16:31769000-31772200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr16:31769200-31773600	Weak transcription	Fetal Heart	heart
9	chr16:31769600-31772000	Weak transcription	Brain Substantia Nigra	brain
10	chr16:31769600-31772200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr16:31769600-31772200	Weak transcription	NH-A	brain
12	chr16:31769800-31772200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr16:31770000-31772000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr16:31770000-31772000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr16:31770000-31772200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr16:31770000-31772200	Weak transcription	Ovary	ovary
17	chr16:31770200-31772000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr16:31770200-31772200	Weak transcription	Left Ventricle	heart
19	chr16:31770200-31773400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr16:31770800-31772000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr16:31770800-31772200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr16:31770800-31772200	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr16:31770800-31772200	Weak transcription	HSMMtube	muscle
24	chr16:31770800-31773400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr16:31770800-31773600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr16:31771000-31772000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr16:31771000-31772000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr16:31771000-31772000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr16:31771000-31772000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr16:31771000-31772000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr16:31771000-31772000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr16:31771000-31772000	Weak transcription	Adipose Nuclei	Adipose
33	chr16:31771000-31772000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr16:31771000-31772000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr16:31771000-31772200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr16:31771000-31772200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr16:31771000-31772200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr16:31771000-31772200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr16:31771800-31772600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
40	chr16:31771800-31772600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
41	chr16:31771800-31786000	ZNF genes & repeats	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links