Variant report

Variant	rs9568728
Chromosome Location	chr13:52946593-52946594
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	chr13:52945253..52946757-chr13:52952983..52954577,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1056335	0.88[ASN][1000 genomes]
rs11148252	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11618716	0.88[ASN][1000 genomes]
rs11620062	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs13431	0.87[ASN][1000 genomes]
rs1815669	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3803262	0.84[ASN][1000 genomes]
rs3803264	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3886077	0.90[AFR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4286007	0.90[ASN][1000 genomes]
rs4884320	0.86[ASN][1000 genomes]
rs4884354	0.86[ASN][1000 genomes]
rs4884452	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4885953	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886018	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886077	0.86[ASN][1000 genomes]
rs61958050	0.87[ASN][1000 genomes]
rs6561665	0.83[ASN][1000 genomes]
rs7323666	0.86[ASN][1000 genomes]
rs7333451	0.83[ASN][1000 genomes]
rs7336679	0.83[ASN][1000 genomes]
rs7399631	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7981732	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7985262	0.87[ASN][1000 genomes]
rs7987115	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7993748	0.82[EUR][1000 genomes]
rs8001624	0.86[ASN][1000 genomes]
rs9379	0.83[ASN][1000 genomes]
rs9526913	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526914	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9536046	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9536048	0.93[ASN][1000 genomes]
rs9536052	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9536066	0.81[EUR][1000 genomes]
rs9536069	0.84[ASN][1000 genomes]
rs9596643	0.80[ASN][1000 genomes]
rs9596648	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9596649	0.80[EUR][1000 genomes]
rs9596651	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9568728	CKAP2	cis	Thyroid	GTEx
rs9568728	NEK3	Cis_1M	lymphoblastoid	RTeQTL
rs9568728	CKAP2	cis	Nerve Tibial	GTEx
rs9568728	CKAP2	cis	Adipose Subcutaneous	GTEx
rs9568728	CKAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs9568728	CKAP2	cis	Artery Tibial	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52934000-52951800	Weak transcription	Fetal Intestine Small	intestine
2	chr13:52944800-52947800	Enhancers	HSMM	muscle
3	chr13:52944800-52949600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr13:52945400-52946600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr13:52945400-52946800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr13:52945400-52947800	Enhancers	NH-A	brain
7	chr13:52945400-52947800	Enhancers	Osteobl	bone
8	chr13:52945400-52948000	Enhancers	HMEC	breast
9	chr13:52945400-52948200	Enhancers	Muscle Satellite Cultured Cells	--
10	chr13:52945400-52949400	Enhancers	HUVEC	blood vessel
11	chr13:52945600-52947800	Enhancers	HSMMtube	muscle
12	chr13:52945800-52946600	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr13:52945800-52946600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr13:52945800-52946600	Enhancers	HepG2	liver
15	chr13:52945800-52946800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr13:52945800-52946800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr13:52945800-52946800	Enhancers	Fetal Muscle Leg	muscle
18	chr13:52945800-52946800	Enhancers	NHLF	lung
19	chr13:52945800-52947600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr13:52945800-52948000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr13:52945800-52948000	Enhancers	NHEK	skin
22	chr13:52945800-52948600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr13:52946000-52946800	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr13:52946000-52947600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr13:52946000-52949600	Weak transcription	Spleen	Spleen
26	chr13:52946000-52951800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr13:52946000-52951800	Weak transcription	Adipose Nuclei	Adipose
28	chr13:52946000-52951800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr13:52946000-52951800	Weak transcription	Left Ventricle	heart
30	chr13:52946000-52951800	Weak transcription	Lung	lung
31	chr13:52946000-52951800	Weak transcription	Pancreas	Pancrea
32	chr13:52946000-52951800	Weak transcription	Right Ventricle	heart
33	chr13:52946000-52952000	Weak transcription	Aorta	Aorta
34	chr13:52946000-52952000	Weak transcription	Ovary	ovary
35	chr13:52946000-52952800	Weak transcription	Gastric	stomach
36	chr13:52946000-52969600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr13:52946200-52951800	Weak transcription	Esophagus	oesophagus
38	chr13:52946200-52951800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr13:52946200-52952000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr13:52946200-52952600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr13:52946200-52979200	Weak transcription	A549	lung
42	chr13:52946400-52947200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr13:52946400-52947200	Weak transcription	NHDF-Ad	bronchial
44	chr13:52946400-52949000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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