Variant report

Variant	rs3803264
Chromosome Location	chr13:52971893-52971894
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	chr13:52969752..52972686-chr13:52972707..52974454,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000199605	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs1056335	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11148252	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11618716	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs11620062	0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs12430144	0.84[CHB][hapmap]
rs12870706	0.83[CHB][hapmap]
rs1327323	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs13431	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1815348	0.89[CHB][hapmap]
rs1815669	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803262	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3886077	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs3892337	0.85[CHB][hapmap]
rs4286007	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4545703	0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs4884320	0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4884354	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4884452	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4885953	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4886018	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4886077	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61958050	0.92[ASN][1000 genomes]
rs6561665	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7321964	0.85[CHB][hapmap]
rs7323666	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7333451	0.89[CEU][hapmap];0.95[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]
rs7336679	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs7399631	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7983971	0.89[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs7985262	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7987115	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7990581	0.85[CHB][hapmap]
rs7993748	0.90[CHB][hapmap]
rs8001624	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9379	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]
rs9526913	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9526914	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535914	0.82[CEU][hapmap]
rs9536046	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9536048	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.99[ASN][1000 genomes]
rs9536052	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9536066	0.85[CHB][hapmap]
rs9536069	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9536079	0.85[CHB][hapmap]
rs9568728	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9568732	0.85[CHB][hapmap]
rs9596643	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9596648	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9596651	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs3803264	CKAP2	cis	multi-tissue	Pritchard
rs3803264	LECT1	cis	parietal	SCAN
rs3803264	CKAP2	cis	Nerve Tibial	GTEx
rs3803264	LOC440138	cis	multi-tissue	Pritchard
rs3803264	CKAP2	cis	Artery Tibial	GTEx
rs3803264	CKAP2	cis	Adipose Subcutaneous	GTEx
rs3803264	ATP7B	cis	cerebellum	SCAN
rs3803264	CKAP2	cis	Thyroid	GTEx
rs3803264	CKAP2	cis	parietal	SCAN
rs3803264	CKAP2	cis	cerebellum	SCAN
rs3803264	HNRNPA1L2	cis	cerebellum	SCAN
rs3803264	VPS36	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52946200-52979200	Weak transcription	A549	lung
2	chr13:52949800-52979000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr13:52956200-52978200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr13:52967000-52972200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
5	chr13:52967800-52978800	Weak transcription	NH-A	brain
6	chr13:52968200-52979600	Weak transcription	Gastric	stomach
7	chr13:52968400-52978600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr13:52968400-52978600	Weak transcription	NHDF-Ad	bronchial
9	chr13:52968800-52972600	Strong transcription	HMEC	breast
10	chr13:52969000-52972200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:52969000-52972400	Strong transcription	Osteobl	bone
12	chr13:52969000-52977600	Strong transcription	HSMM	muscle
13	chr13:52969200-52972000	Strong transcription	HSMMtube	muscle
14	chr13:52969200-52972200	Strong transcription	NHEK	skin
15	chr13:52969200-52972400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:52969200-52972600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:52969400-52972600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr13:52969400-52974400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr13:52969600-52978600	Weak transcription	Fetal Brain Male	brain
20	chr13:52969800-52973200	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr13:52970000-52979200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr13:52970000-52979400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr13:52970200-52972600	Weak transcription	Brain Hippocampus Middle	brain
24	chr13:52970200-52973000	Weak transcription	Brain Anterior Caudate	brain
25	chr13:52970200-52973400	Weak transcription	Fetal Brain Female	brain
26	chr13:52970200-52977200	Weak transcription	Adipose Nuclei	Adipose
27	chr13:52970200-52979400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr13:52970200-52979400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr13:52970400-52978200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr13:52970800-52972200	Strong transcription	HUVEC	blood vessel
31	chr13:52971200-52972000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr13:52971200-52972000	Strong transcription	NHLF	lung
33	chr13:52971200-52972200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr13:52971400-52972200	Genic enhancers	Left Ventricle	heart
35	chr13:52971400-52972400	Genic enhancers	Lung	lung
36	chr13:52971600-52972200	Genic enhancers	Spleen	Spleen
37	chr13:52971600-52972600	Genic enhancers	Fetal Muscle Leg	muscle
38	chr13:52971600-52972800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr13:52971800-52972000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr13:52971800-52972000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr13:52971800-52972000	Enhancers	Right Ventricle	heart
42	chr13:52971800-52972200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr13:52971800-52972200	Enhancers	Right Atrium	heart
44	chr13:52971800-52972600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr13:52971800-52979600	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links