Variant report

Variant	rs6883445
Chromosome Location	chr5:126761536-126761537
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: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11241930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11745840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11747639	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11950427	0.90[YRI][hapmap]
rs11950754	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11950816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12233927	0.82[YRI][hapmap]
rs1587628	0.83[EUR][1000 genomes]
rs1592960	0.83[EUR][1000 genomes]
rs17164922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17164923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17164951	0.92[YRI][hapmap]
rs17164956	0.81[YRI][hapmap]
rs17164957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17165013	1.00[CEU][hapmap]
rs17165018	1.00[CEU][hapmap]
rs17165090	0.82[YRI][hapmap]
rs17684740	1.00[CEU][hapmap]
rs17685202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1990954	1.00[CEU][hapmap]
rs2134252	0.83[EUR][1000 genomes]
rs2270933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3851469	0.90[YRI][hapmap]
rs41298320	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55861432	0.83[EUR][1000 genomes]
rs57626860	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6595773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6897163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73331215	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7737871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][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:44 , 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	chr5:126757400-126761600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:126759200-126774000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:126759800-126761800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:126760200-126761600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:126760200-126761800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:126760200-126764400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr5:126760400-126761600	Enhancers	Adipose Nuclei	Adipose
18	chr5:126760400-126764200	Enhancers	Fetal Heart	heart
19	chr5:126760400-126778600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:126760600-126764000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:126760600-126766200	Enhancers	Brain Hippocampus Middle	brain
22	chr5:126760800-126761800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:126760800-126761800	Enhancers	Right Atrium	heart
24	chr5:126760800-126763400	Genic enhancers	Fetal Muscle Leg	muscle
25	chr5:126761000-126761800	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr5:126761000-126761800	Enhancers	Left Ventricle	heart
27	chr5:126761000-126762800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:126761000-126763400	Enhancers	Right Ventricle	heart
29	chr5:126761000-126774800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:126761000-126783400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr5:126761200-126761600	Enhancers	Primary hematopoietic stem cells	blood
32	chr5:126761200-126761600	Weak transcription	Fetal Intestine Small	intestine
33	chr5:126761200-126762400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr5:126761200-126762400	Weak transcription	Pancreas	Pancrea
35	chr5:126761200-126763200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:126761200-126763200	Weak transcription	Brain Substantia Nigra	brain
37	chr5:126761200-126763400	Weak transcription	Brain Anterior Caudate	brain
38	chr5:126761200-126763600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr5:126761200-126763600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:126761200-126764000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:126761200-126764800	Weak transcription	HSMM	muscle
42	chr5:126761400-126761600	Strong transcription	HSMMtube	muscle
43	chr5:126761400-126761800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr5:126761400-126763200	Weak transcription	Fetal Intestine Large	intestine

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