Variant report

Variant	rs3825527
Chromosome Location	chr13:52545141-52545142
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52543974..52546024-chr13:52586365..52587928,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253710	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1051332	0.81[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11616964	0.82[AMR][1000 genomes]
rs11620583	0.85[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes]
rs1801243	0.96[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.80[LWK][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1801244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1886547	0.82[CEU][hapmap]
rs1924611	0.85[CEU][hapmap];0.90[AMR][1000 genomes]
rs1951922	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2004866	0.85[CEU][hapmap];0.80[GIH][hapmap];0.82[AMR][1000 genomes]
rs2104353	0.84[EUR][1000 genomes]
rs2147363	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2181891	0.96[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2296246	0.85[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2408544	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs2408550	0.82[CEU][hapmap]
rs3742288	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783241	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3825526	0.85[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3825528	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs4297592	0.82[CEU][hapmap]
rs7327634	0.85[CEU][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs747781	0.96[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes]
rs750290	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs752570	0.85[EUR][1000 genomes]
rs754610	0.85[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs755363	0.82[CEU][hapmap]
rs7991237	0.82[CEU][hapmap];0.86[MEX][hapmap]
rs7994928	0.89[AMR][1000 genomes]
rs7995946	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs7999812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316562	0.81[EUR][1000 genomes]
rs9316563	0.85[CEU][hapmap];0.90[AMR][1000 genomes]
rs9526811	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9526812	0.85[CEU][hapmap];0.92[GIH][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs9526814	0.89[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9526819	0.85[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes]
rs9526821	0.82[AMR][1000 genomes]
rs9526837	0.82[CEU][hapmap]
rs9535797	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9535812	1.00[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9535817	0.85[AMR][1000 genomes]
rs9535819	0.90[AMR][1000 genomes]
rs9535822	0.85[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.89[AMR][1000 genomes]
rs9535823	0.90[AMR][1000 genomes]
rs9535826	0.85[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap];0.90[AMR][1000 genomes]
rs9535828	0.85[CEU][hapmap];0.88[MEX][hapmap];0.87[AMR][1000 genomes]
rs9535829	0.82[AMR][1000 genomes]
rs9535833	0.82[AMR][1000 genomes]
rs9535836	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs9535851	0.82[CEU][hapmap]
rs9535858	0.82[CEU][hapmap]
rs9535862	0.82[CEU][hapmap]
rs9535866	0.82[CEU][hapmap]
rs9563078	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs9563084	0.82[AMR][1000 genomes]
rs9563089	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs9568677	0.85[CEU][hapmap];0.92[GIH][hapmap];0.91[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs9568681	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9568713	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	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
5	nsv455888	chr13:52491193-52570728	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv561649	chr13:52491193-52570728	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv1041996	chr13:52544805-52581501	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
8	esv2763022	chr13:52544978-52581513	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription 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	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3825527	NCRNA00282	cis	cerebellum	SCAN
rs3825527	CKAP2	cis	parietal	SCAN
rs3825527	CKAP2	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr13:52509200-52549800	Weak transcription	Brain Substantia Nigra	brain
4	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:52509400-52548600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr13:52513200-52553000	Weak transcription	Placenta	Placenta
7	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
8	chr13:52516000-52548000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr13:52516600-52554000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:52516800-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr13:52519400-52546000	Weak transcription	Spleen	Spleen
12	chr13:52520600-52553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr13:52525200-52550200	Weak transcription	Fetal Brain Female	brain
14	chr13:52525400-52553000	Weak transcription	Ovary	ovary
15	chr13:52529600-52553000	Weak transcription	Psoas Muscle	Psoas
16	chr13:52530200-52555400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr13:52530400-52549000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr13:52530600-52550400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr13:52530800-52553000	Weak transcription	Fetal Lung	lung
20	chr13:52532800-52548200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr13:52532800-52553000	Weak transcription	Fetal Muscle Trunk	muscle
22	chr13:52534400-52555400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr13:52534600-52546000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr13:52536200-52548400	Weak transcription	Colonic Mucosa	Colon
25	chr13:52537000-52552800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr13:52539800-52545800	Weak transcription	Right Ventricle	heart
27	chr13:52540000-52554600	Weak transcription	HSMMtube	muscle
28	chr13:52540400-52545200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr13:52540400-52550400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr13:52541000-52553000	Weak transcription	Left Ventricle	heart
31	chr13:52541400-52554800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:52541800-52546000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr13:52541800-52546800	Enhancers	Stomach Mucosa	stomach
34	chr13:52541800-52553000	Weak transcription	Right Atrium	heart
35	chr13:52542400-52547000	Weak transcription	Esophagus	oesophagus
36	chr13:52542400-52551400	Weak transcription	Lung	lung
37	chr13:52542800-52549600	Weak transcription	Brain Germinal Matrix	brain
38	chr13:52542800-52549600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr13:52542800-52550200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr13:52542800-52551000	Weak transcription	Fetal Muscle Leg	muscle
41	chr13:52543000-52548200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr13:52543400-52546800	Genic enhancers	Fetal Intestine Small	intestine
43	chr13:52543600-52545200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr13:52543600-52545200	Enhancers	Fetal Heart	heart
45	chr13:52543600-52548000	Weak transcription	Fetal Stomach	stomach
46	chr13:52543800-52545200	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr13:52543800-52545200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr13:52543800-52545400	Enhancers	Primary T cells from cord blood	blood
49	chr13:52543800-52545400	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr13:52543800-52546000	Enhancers	Primary T helper cells PMA-I stimulated	--

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