Variant report

Variant	rs4885325
Chromosome Location	chr13:53171317-53171318
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	chr13:53169737..53172275-chr13:53234901..53237385,2	MCF-7	breast:

Extended variants
information (count: 79 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1057478	0.90[ASW][hapmap];0.84[CHB][hapmap];0.82[MKK][hapmap];0.86[YRI][hapmap]
rs11148252	0.91[ASW][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap]
rs11148260	0.85[ASN][1000 genomes]
rs11616261	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11616459	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs11617331	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11618716	0.81[ASW][hapmap];0.83[LWK][hapmap];0.84[MKK][hapmap]
rs1811894	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1811895	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1924036	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[YRI][hapmap]
rs2038826	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2147676	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap]
rs2147692	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.85[ASN][1000 genomes]
rs2575960	1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs2760815	0.83[CEU][hapmap]
rs342768	0.82[ASN][1000 genomes]
rs342770	0.82[ASN][1000 genomes]
rs3742297	0.90[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.86[ASN][1000 genomes]
rs4284531	0.84[CHB][hapmap]
rs4286007	0.81[ASW][hapmap];0.86[LWK][hapmap];0.84[MKK][hapmap]
rs4301905	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4335671	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4884235	0.81[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap]
rs4886018	0.91[ASW][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap]
rs55688428	0.85[ASN][1000 genomes]
rs61958118	0.91[AFR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959716	0.84[ASN][1000 genomes]
rs6561671	0.84[ASN][1000 genomes]
rs6561675	0.80[ASN][1000 genomes]
rs7139495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7139630	1.00[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap]
rs7328729	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap]
rs7334137	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs7334677	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs7336771	1.00[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs7399901	0.83[ASN][1000 genomes]
rs7990581	0.81[ASW][hapmap]
rs7997186	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7999849	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9526913	0.81[ASW][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap]
rs9526951	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9526968	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9526974	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9526975	0.90[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];0.80[TSI][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs9526982	0.84[ASN][1000 genomes]
rs9536066	0.81[ASW][hapmap]
rs9536104	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];0.93[YRI][hapmap]
rs9536197	0.84[ASN][1000 genomes]
rs9536202	0.85[ASN][1000 genomes]
rs9536211	0.94[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536212	0.92[CHB][hapmap];0.81[JPT][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536217	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9536219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536220	0.82[CHB][hapmap];0.81[YRI][hapmap]
rs9536223	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9536236	0.84[ASN][1000 genomes]
rs9536247	0.86[ASN][1000 genomes]
rs9536262	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.86[YRI][hapmap];0.83[ASN][1000 genomes]
rs9563113	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap]
rs9563114	1.00[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap]
rs9568732	0.81[ASW][hapmap]
rs9568734	0.81[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
5	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
6	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
7	nsv1038132	chr13:53057359-53190994	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv820041	chr13:53061338-53280588	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv1044949	chr13:53071140-53289426	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	esv2760295	chr13:53071152-53178504	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv900087	chr13:53119704-53208030	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv976118	chr13:53120951-53171671	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv819201	chr13:53137490-53240330	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv1044051	chr13:53139132-53287023	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
15	nsv1038942	chr13:53139132-53289426	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
16	nsv1039911	chr13:53139132-53303074	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
17	esv13738	chr13:53159859-53177755	Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4885325	CKAP2	cis	Artery Tibial	GTEx
rs4885325	HNRNPA1L2	cis	cerebellum	SCAN
rs4885325	CKAP2	cis	parietal	SCAN
rs4885325	SUGT1	cis	cerebellum	SCAN
rs4885325	CKAP2	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53161000-53173000	Weak transcription	Fetal Heart	heart
2	chr13:53167600-53171400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr13:53168400-53173000	Weak transcription	Osteobl	bone
4	chr13:53168800-53172800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr13:53169000-53171400	Weak transcription	HepG2	liver
6	chr13:53169000-53174000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr13:53169400-53173200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr13:53170200-53172800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr13:53170800-53172400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr13:53171000-53171400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:53171200-53173800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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