Variant report

Variant	rs4886018
Chromosome Location	chr13:52990717-52990718
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	chr13:52989175..52991145-chr13:53028466..53031085,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136108	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1056335	0.82[CEU][hapmap];0.95[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]
rs11148252	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11618716	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11620062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12430144	0.85[CHB][hapmap]
rs12870706	0.85[CHB][hapmap]
rs1327323	0.90[CHB][hapmap];0.88[CHD][hapmap];0.89[JPT][hapmap];0.80[MEX][hapmap]
rs13431	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1815669	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3803262	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3803264	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs3886077	0.91[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3892337	0.88[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes]
rs4286007	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4545703	0.85[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[YRI][hapmap]
rs4884320	1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs4884354	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4884452	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4885953	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886077	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61958050	0.93[ASN][1000 genomes]
rs6561665	0.95[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.80[MEX][hapmap]
rs7321964	0.89[CEU][hapmap];0.90[CHB][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.81[TSI][hapmap]
rs7323666	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7328653	0.80[EUR][1000 genomes]
rs7333451	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7336679	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs7399631	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7985262	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7987115	1.00[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.84[TSI][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7990581	0.91[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs7993748	0.91[ASW][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap];0.94[YRI][hapmap]
rs8001624	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]
rs9379	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]
rs9526913	0.91[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs9526914	0.91[ASN][1000 genomes]
rs9535914	0.89[CEU][hapmap];0.83[JPT][hapmap]
rs9536046	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9536048	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9536052	0.95[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9536066	0.91[ASW][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs9536069	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9536079	0.90[ASW][hapmap];0.81[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.83[LWK][hapmap];0.87[MKK][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes]
rs9536104	0.83[LWK][hapmap];0.83[MKK][hapmap]
rs9568728	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9568732	0.91[ASW][hapmap];0.89[CEU][hapmap];0.90[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9568734	0.91[ASW][hapmap];0.89[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.84[JPT][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9596643	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs9596648	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs9596651	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]

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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4886018	WDFY2	cis	cerebellum	SCAN
rs4886018	CKAP2	cis	Nerve Tibial	GTEx
rs4886018	CKAP2	cis	lung	GTEx
rs4886018	CKAP2	cis	parietal	SCAN
rs4886018	CKAP2	cis	Thyroid	GTEx
rs4886018	CKAP2	cis	Skin Sun Exposed Lower leg	GTEx
rs4886018	CKAP2	cis	Artery Tibial	GTEx
rs4886018	HNRNPA1L2	cis	cerebellum	SCAN
rs4886018	VPS36	cis	cerebellum	SCAN
rs4886018	CKAP2	cis	cerebellum	SCAN
rs4886018	CKAP2	cis	Muscle Skeletal	GTEx
rs4886018	CKAP2	cis	Heart Left Ventricle	GTEx
rs4886018	CKAP2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52980200-53002000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr13:52980200-53021600	Weak transcription	Small Intestine	intestine
3	chr13:52980800-52992800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr13:52980800-52993200	Weak transcription	Right Atrium	heart
5	chr13:52981000-53022800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr13:52982800-52996400	Weak transcription	Brain Germinal Matrix	brain
7	chr13:52982800-53012600	Weak transcription	Fetal Brain Male	brain
8	chr13:52983600-53000800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr13:52983800-53016600	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr13:52984000-52996600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr13:52984000-53002400	Weak transcription	Hela-S3	cervix
12	chr13:52984400-53023400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr13:52984600-52991000	Strong transcription	Primary hematopoietic stem cells	blood
14	chr13:52984600-52993200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr13:52984800-53013400	Strong transcription	Dnd41	blood
16	chr13:52985000-52993600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr13:52985000-53000600	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr13:52985000-53001400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr13:52985000-53002400	Weak transcription	K562	blood
20	chr13:52985000-53013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr13:52985000-53017400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr13:52985000-53019400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr13:52985200-52991400	Strong transcription	Primary B cells from cord blood	blood
24	chr13:52985200-52993600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr13:52985600-52994200	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr13:52985600-53000800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr13:52985600-53004000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr13:52985600-53010600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr13:52985800-52993400	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr13:52985800-52993600	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr13:52985800-52994000	Strong transcription	Duodenum Mucosa	Duodenum
32	chr13:52985800-52994400	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr13:52985800-53001400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr13:52986000-53017000	Strong transcription	Primary B cells from peripheral blood	blood
35	chr13:52986200-52993400	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr13:52986200-53001600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr13:52986400-52993600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr13:52986600-52993400	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr13:52986600-52994000	Strong transcription	Fetal Intestine Large	intestine
40	chr13:52986600-53013400	Strong transcription	Liver	Liver
41	chr13:52986800-53002400	Weak transcription	Stomach Mucosa	stomach
42	chr13:52987000-53004200	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr13:52987200-53023600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr13:52987400-52992600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr13:52987800-52990800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr13:52987800-52991000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr13:52987800-52992200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr13:52987800-52992600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr13:52988000-53001200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr13:52988200-52991000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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