Variant report

Variant	rs72790417
Chromosome Location	chr5:126761374-126761375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126753682..126756531-chr5:126759834..126762249,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17444885	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17604615	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17604665	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604777	1.00[ASN][1000 genomes]
rs17604819	1.00[ASN][1000 genomes]
rs17604882	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17604889	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17604946	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17673474	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17673517	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17673685	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17673995	0.89[EUR][1000 genomes]
rs2068168	1.00[ASN][1000 genomes]
rs3812053	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812054	1.00[ASN][1000 genomes]
rs41298308	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41298312	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57256097	0.88[EUR][1000 genomes]
rs6595768	1.00[ASN][1000 genomes]
rs6882034	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6892742	0.87[ASN][1000 genomes]
rs72788576	0.86[ASN][1000 genomes]
rs72788578	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72788581	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72788599	1.00[ASN][1000 genomes]
rs72790405	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790408	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790410	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790411	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790412	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790418	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790419	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790428	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790430	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790433	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790438	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790444	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790451	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72790460	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72790468	0.91[EUR][1000 genomes]
rs72790470	0.91[EUR][1000 genomes]
rs72790475	0.91[EUR][1000 genomes]
rs72790483	0.89[EUR][1000 genomes]
rs72790485	0.89[EUR][1000 genomes]
rs72790487	0.83[EUR][1000 genomes]
rs73786108	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7718640	0.89[EUR][1000 genomes]
rs7730171	0.86[EUR][1000 genomes]
rs7731380	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 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	chr5:126742800-126762600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr5:126742800-126782000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:126742800-126792400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:126743000-126784800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr5:126755000-126761800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr5:126755400-126774400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:126755800-126763200	Weak transcription	Brain Angular Gyrus	brain
8	chr5:126756000-126768000	Weak transcription	Fetal Brain Male	brain
9	chr5:126756000-126770400	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:126756800-126763600	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:126757400-126761400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:126757400-126761600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:126759200-126774000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:126759800-126761800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:126760200-126761600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:126760200-126761800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:126760200-126764400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr5:126760400-126761600	Enhancers	Adipose Nuclei	Adipose
19	chr5:126760400-126764200	Enhancers	Fetal Heart	heart
20	chr5:126760400-126778600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr5:126760600-126764000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:126760600-126766200	Enhancers	Brain Hippocampus Middle	brain
23	chr5:126760800-126761800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:126760800-126761800	Enhancers	Right Atrium	heart
25	chr5:126760800-126763400	Genic enhancers	Fetal Muscle Leg	muscle
26	chr5:126761000-126761800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr5:126761000-126761800	Enhancers	Left Ventricle	heart
28	chr5:126761000-126762800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr5:126761000-126763400	Enhancers	Right Ventricle	heart
30	chr5:126761000-126774800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr5:126761000-126783400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr5:126761200-126761400	Weak transcription	HSMMtube	muscle
33	chr5:126761200-126761600	Enhancers	Primary hematopoietic stem cells	blood
34	chr5:126761200-126761600	Weak transcription	Fetal Intestine Small	intestine
35	chr5:126761200-126762400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:126761200-126762400	Weak transcription	Pancreas	Pancrea
37	chr5:126761200-126763200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr5:126761200-126763200	Weak transcription	Brain Substantia Nigra	brain
39	chr5:126761200-126763400	Weak transcription	Brain Anterior Caudate	brain
40	chr5:126761200-126763600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr5:126761200-126763600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr5:126761200-126764000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr5:126761200-126764800	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links