Variant report

Variant	rs7329039
Chromosome Location	chr13:49145238-49145239
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:49143466..49145650-chr13:49355908..49357695,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1547660	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1926595	1.00[ASN][1000 genomes]
rs1926596	0.91[ASN][1000 genomes]
rs1926597	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs198564	0.85[ASN][1000 genomes]
rs198568	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs198571	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs198574	0.88[ASN][1000 genomes]
rs198575	0.88[ASN][1000 genomes]
rs198576	0.88[ASN][1000 genomes]
rs198577	0.88[ASN][1000 genomes]
rs2274400	0.91[ASN][1000 genomes]
rs28414460	0.91[ASN][1000 genomes]
rs28646083	0.91[ASN][1000 genomes]
rs28674973	0.84[ASN][1000 genomes]
rs2897587	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs3092898	0.88[ASN][1000 genomes]
rs3751380	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs398158	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs403390	0.88[ASN][1000 genomes]
rs425834	0.81[AMR][1000 genomes]
rs61074776	1.00[ASN][1000 genomes]
rs6561448	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6561457	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6561461	1.00[ASN][1000 genomes]
rs7325962	0.83[ASN][1000 genomes]
rs7329865	0.84[ASN][1000 genomes]
rs73486867	1.00[ASN][1000 genomes]
rs73495016	0.88[ASN][1000 genomes]
rs7985825	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7987935	0.91[ASN][1000 genomes]
rs7992129	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7995216	0.97[ASN][1000 genomes]
rs7996186	0.91[ASN][1000 genomes]
rs7996402	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7998781	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8001241	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002565	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316385	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9316401	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9331959	0.91[ASN][1000 genomes]
rs9331965	0.88[ASN][1000 genomes]
rs9331973	0.91[ASN][1000 genomes]
rs9332054	0.83[ASN][1000 genomes]
rs9591172	1.00[ASN][1000 genomes]
rs9591177	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9591178	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9595929	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832602	chr13:49003159-49167781	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	14 gene(s)	inside rSNPs	diseases
3	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv455881	chr13:49134412-49169570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv561591	chr13:49134412-49169570	Weak transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49135000-49155000	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr13:49137200-49153000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr13:49138800-49145600	Weak transcription	HUVEC	blood vessel
4	chr13:49140800-49146400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr13:49141200-49147000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr13:49141400-49145800	Enhancers	Fetal Stomach	stomach
7	chr13:49141400-49146200	Enhancers	HepG2	liver
8	chr13:49141400-49146400	Enhancers	Fetal Lung	lung
9	chr13:49141400-49146600	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr13:49141800-49145600	Enhancers	Dnd41	blood
11	chr13:49141800-49145800	Enhancers	Placenta	Placenta
12	chr13:49141800-49146000	Enhancers	Fetal Muscle Leg	muscle
13	chr13:49141800-49150200	Weak transcription	Aorta	Aorta
14	chr13:49142200-49146000	Enhancers	Spleen	Spleen
15	chr13:49142400-49145800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr13:49142400-49148800	Enhancers	Fetal Thymus	thymus
17	chr13:49142600-49145400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:49142600-49145400	Enhancers	Esophagus	oesophagus
19	chr13:49142600-49145400	Enhancers	Skeletal Muscle Male	skeletal muscle
20	chr13:49142600-49145400	Enhancers	HSMMtube	muscle
21	chr13:49142600-49145600	Enhancers	Adipose Nuclei	Adipose
22	chr13:49142600-49145600	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr13:49142600-49145600	Enhancers	Stomach Smooth Muscle	stomach
24	chr13:49142800-49145600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr13:49142800-49145600	Enhancers	Brain Hippocampus Middle	brain
26	chr13:49143000-49153600	Weak transcription	Liver	Liver
27	chr13:49143400-49145600	Weak transcription	Stomach Mucosa	stomach
28	chr13:49143600-49146000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr13:49143600-49147800	Enhancers	Fetal Muscle Trunk	muscle
30	chr13:49143600-49148800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr13:49143800-49145600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:49143800-49145600	Enhancers	GM12878-XiMat	blood
33	chr13:49143800-49145800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr13:49144000-49146200	Enhancers	Primary T cells fromperipheralblood	blood
35	chr13:49144000-49147800	Enhancers	Primary hematopoietic stem cells	blood
36	chr13:49144000-49151400	Weak transcription	Lung	lung
37	chr13:49144200-49145400	Weak transcription	Brain Anterior Caudate	brain
38	chr13:49144200-49145400	Weak transcription	Brain Substantia Nigra	brain
39	chr13:49144200-49145600	Enhancers	K562	blood
40	chr13:49144200-49145800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr13:49144400-49145400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr13:49144400-49145400	Enhancers	NHDF-Ad	bronchial
43	chr13:49144400-49145600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr13:49144400-49146000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr13:49144400-49146000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr13:49144400-49146200	Bivalent Enhancer	Primary B cells from cord blood	blood
47	chr13:49144400-49146200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr13:49144400-49146200	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr13:49144600-49145600	Enhancers	Colon Smooth Muscle	Colon
50	chr13:49144600-49145600	Enhancers	Duodenum Smooth Muscle	Duodenum

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