Variant report

Variant	rs8001624
Chromosome Location	chr13:53002995-53002996
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	chr13:53000967..53003487-chr13:53023394..53025748,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136100	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 15 )

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

rs_ID	r²[population]
rs1056335	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11148252	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11618716	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs11620062	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12430144	0.85[CHB][hapmap]
rs12870706	0.85[CHB][hapmap]
rs1327323	0.88[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap]
rs13431	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1815669	0.86[ASN][1000 genomes]
rs3803262	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3803264	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]
rs3886077	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs3892337	0.90[CHB][hapmap]
rs4286007	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4884320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4884354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4884452	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs4885953	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4886018	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4886077	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61958050	0.99[ASN][1000 genomes]
rs6561665	0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs7321964	0.90[CHB][hapmap]
rs7323666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7333451	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];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7336679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7399631	0.85[ASN][1000 genomes]
rs7985262	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7987115	0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7990581	0.90[CHB][hapmap]
rs7993748	0.95[CHB][hapmap]
rs9379	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	0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs9526914	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9536046	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[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];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9536048	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9536052	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9536066	0.90[CHB][hapmap]
rs9536069	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9536079	0.90[CHB][hapmap]
rs9568728	0.86[ASN][1000 genomes]
rs9568732	0.90[CHB][hapmap]
rs9568734	0.85[CHB][hapmap]
rs9596643	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap]
rs9596648	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9596651	0.95[CHB][hapmap];0.94[JPT][hapmap]

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	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	esv3434605	chr13:52999509-53034851	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	n/a

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs8001624	WDFY2	cis	cerebellum	SCAN
rs8001624	CKAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs8001624	VPS36	cis	Esophagus Mucosa	GTEx
rs8001624	CKAP2	cis	cerebellum	SCAN
rs8001624	VPS36	cis	cerebellum	SCAN
rs8001624	HNRNPA1L2	cis	cerebellum	SCAN
rs8001624	CKAP2	cis	Adipose Subcutaneous	GTEx
rs8001624	ATP7B	cis	cerebellum	SCAN
rs8001624	CKAP2	cis	Artery Tibial	GTEx
rs8001624	CKAP2	cis	parietal	SCAN
rs8001624	CKAP2	cis	Heart Left Ventricle	GTEx
rs8001624	CKAP2	cis	Nerve Tibial	GTEx
rs8001624	CKAP2	cis	Thyroid	GTEx
rs8001624	CKAP2	cis	Muscle Skeletal	GTEx
rs8001624	LECT1	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52980200-53021600	Weak transcription	Small Intestine	intestine
2	chr13:52981000-53022800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr13:52982800-53012600	Weak transcription	Fetal Brain Male	brain
4	chr13:52983800-53016600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr13:52984400-53023400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr13:52984800-53013400	Strong transcription	Dnd41	blood
7	chr13:52985000-53013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr13:52985000-53017400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr13:52985000-53019400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr13:52985600-53004000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr13:52985600-53010600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr13:52986000-53017000	Strong transcription	Primary B cells from peripheral blood	blood
13	chr13:52986600-53013400	Strong transcription	Liver	Liver
14	chr13:52987000-53004200	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr13:52987200-53023600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr13:52988800-53010000	Weak transcription	Esophagus	oesophagus
17	chr13:52989000-53003400	Weak transcription	Gastric	stomach
18	chr13:52989000-53006000	Weak transcription	NHLF	lung
19	chr13:52989000-53015000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr13:52989000-53016200	Strong transcription	Adipose Nuclei	Adipose
21	chr13:52989000-53021600	Weak transcription	Fetal Heart	heart
22	chr13:52989000-53022800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:52989400-53003400	Weak transcription	Spleen	Spleen
24	chr13:52989400-53015000	Weak transcription	Lung	lung
25	chr13:52990400-53003000	Weak transcription	Brain Angular Gyrus	brain
26	chr13:52990800-53015000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr13:52991000-53007200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr13:52991200-53017000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr13:52991600-53008800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr13:52993200-53004400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr13:52993200-53010000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr13:52993400-53003400	Weak transcription	Pancreas	Pancrea
33	chr13:52993400-53008000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr13:52993400-53008400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr13:52993400-53008400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr13:52993600-53003400	Weak transcription	Right Atrium	heart
37	chr13:52993800-53003200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr13:52993800-53003200	Weak transcription	Brain Substantia Nigra	brain
39	chr13:52993800-53003200	Weak transcription	Colonic Mucosa	Colon
40	chr13:52994200-53003200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr13:52995000-53017800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr13:52995200-53023800	Weak transcription	Aorta	Aorta
43	chr13:52995600-53008800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr13:52995800-53019800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr13:52995800-53023800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr13:52996000-53004200	Strong transcription	HSMM	muscle
47	chr13:52996200-53011200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr13:52997000-53003200	Weak transcription	Brain Anterior Caudate	brain
49	chr13:52997000-53005000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr13:52997200-53003200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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