Variant report

Variant	rs9379
Chromosome Location	chr13:53050479-53050480
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	chr13:53049275..53051586-chr13:53052175..53054640,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1056335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11148252	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11618716	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11620062	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs1327323	0.88[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs13431	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1815669	0.84[ASN][1000 genomes]
rs2575960	0.82[ASW][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap]
rs3803262	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3803264	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs3886077	0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs3892337	0.86[CHB][hapmap]
rs4286007	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs4884320	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4884354	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4884452	0.90[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.83[ASN][1000 genomes]
rs4885953	0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4886018	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886077	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61958050	0.96[ASN][1000 genomes]
rs6561665	0.89[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7321964	0.86[CHB][hapmap]
rs7323666	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7333451	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7336679	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7399631	0.83[ASN][1000 genomes]
rs7985262	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7987115	0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs7990581	0.86[CHB][hapmap]
rs7993748	0.90[CHB][hapmap]
rs8001624	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526913	0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs9526914	0.90[ASN][1000 genomes]
rs9536046	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs9536048	0.90[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9536052	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs9536066	0.86[CHB][hapmap]
rs9536069	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9536079	0.86[CHB][hapmap]
rs9563114	0.89[LWK][hapmap];0.90[MKK][hapmap]
rs9568728	0.83[ASN][1000 genomes]
rs9568732	0.86[CHB][hapmap]
rs9568734	0.90[CHB][hapmap]
rs9596643	0.87[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs9596648	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9596651	0.90[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
2	nsv1040931	chr13:52564792-53350914	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv541773	chr13:52564792-53350914	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv428288	chr13:52728370-53068132	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv900084	chr13:52835231-53119704	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1838257	chr13:52971893-53231454	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv900085	chr13:53022518-53216622	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv900086	chr13:53030565-53208030	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9379	WDFY2	cis	cerebellum	SCAN
rs9379	CKAP2	cis	parietal	SCAN
rs9379	CKAP2	cis	Muscle Skeletal	GTEx
rs9379	CKAP2	cis	Thyroid	GTEx
rs9379	CKAP2	cis	Heart Left Ventricle	GTEx
rs9379	VPS36	cis	cerebellum	SCAN
rs9379	CKAP2	cis	Nerve Tibial	GTEx
rs9379	CKAP2	cis	Artery Tibial	GTEx
rs9379	CKAP2	cis	Adipose Subcutaneous	GTEx
rs9379	LECT1	cis	parietal	SCAN
rs9379	CKAP2	cis	cerebellum	SCAN
rs9379	CKAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs9379	HNRNPA1L2	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53030200-53050800	Weak transcription	Gastric	stomach
2	chr13:53030200-53052600	Weak transcription	Spleen	Spleen
3	chr13:53030200-53053800	Weak transcription	Small Intestine	intestine
4	chr13:53030400-53055800	Weak transcription	Lung	lung
5	chr13:53030600-53050600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr13:53030600-53050800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr13:53030600-53050800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr13:53030600-53051400	Weak transcription	Fetal Brain Male	brain
9	chr13:53030600-53052400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr13:53030600-53052800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr13:53031000-53050800	Weak transcription	Stomach Mucosa	stomach
12	chr13:53031000-53051200	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr13:53031000-53051400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr13:53032600-53052200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr13:53033800-53051600	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr13:53034200-53050800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr13:53034200-53052000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr13:53034400-53054400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr13:53035000-53051400	Strong transcription	Osteobl	bone
20	chr13:53036000-53050600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr13:53036000-53050800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr13:53036000-53052600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr13:53036200-53051200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr13:53036800-53053000	Weak transcription	Brain Germinal Matrix	brain
25	chr13:53037000-53051400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr13:53037600-53052000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr13:53038000-53053200	Weak transcription	Brain Angular Gyrus	brain
28	chr13:53038200-53051200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr13:53038200-53051800	Strong transcription	Dnd41	blood
30	chr13:53038200-53055400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr13:53039200-53051600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr13:53039800-53052800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr13:53041000-53051400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr13:53041000-53052000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr13:53041200-53051400	Weak transcription	NHLF	lung
36	chr13:53041200-53052200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr13:53041200-53053200	Weak transcription	Fetal Stomach	stomach
38	chr13:53041400-53052600	Weak transcription	Placenta	Placenta
39	chr13:53042800-53054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr13:53043000-53052800	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr13:53043200-53052400	Weak transcription	Fetal Heart	heart
42	chr13:53043600-53051400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr13:53043600-53052800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr13:53044400-53051400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr13:53044600-53051800	Strong transcription	HMEC	breast
46	chr13:53044800-53051200	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr13:53045200-53051200	Strong transcription	Primary B cells from cord blood	blood
48	chr13:53045400-53051600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr13:53045400-53051600	Strong transcription	Fetal Intestine Large	intestine
50	chr13:53045600-53051000	Strong transcription	HUES6 Cell Line	embryonic stem cell

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