Variant report

Variant	rs9535812
Chromosome Location	chr13:52550735-52550736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr13:52550668-52550803	MCF10A-Er-Src	breast:	n/a	n/a
2	JUND	chr13:52550550-52550892	Hela-S3	cervix:	n/a	chr13:52550709-52550720
3	FOS	chr13:52550682-52550802	MCF10A-Er-Src	breast:	n/a	n/a
4	JUN	chr13:52550539-52550883	HepG2	liver:	n/a	n/a
5	JUN	chr13:52550648-52550835	K562	blood:	n/a	n/a
6	JUND	chr13:52550547-52550892	HepG2	liver:	n/a	chr13:52550709-52550720
7	ATF1	chr13:52550582-52550871	K562	blood:	n/a	n/a
8	FOS	chr13:52550563-52550868	MCF10A-Er-Src	breast:	n/a	n/a
9	JUND	chr13:52550540-52550890	K562	blood:	n/a	chr13:52550709-52550720
10	FOS	chr13:52550588-52550848	MCF10A-Er-Src	breast:	n/a	n/a
11	JUND	chr13:52550422-52551057	SK-N-SH	brain:	n/a	chr13:52550709-52550720

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:52549808..52551859-chr13:52553072..52555669,2	K562	blood:
2	chr13:52550522..52553056-chr13:52572837..52575567,2	MCF-7	breast:

Variant related genes	Relation type
ATP7B	TF binding region

Extended variants
information (count: 119 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1004576	0.91[CHB][hapmap]
rs1051332	0.82[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs1055062	0.91[CHB][hapmap]
rs1060631	0.91[CHB][hapmap]
rs11616964	0.88[AMR][1000 genomes]
rs11620583	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12146904	0.91[CHB][hapmap]
rs12431310	0.91[CHB][hapmap]
rs1571189	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs1801243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1801244	1.00[ASW][hapmap];0.96[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1886538	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs1886542	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs1886543	0.91[CHB][hapmap]
rs1886544	0.91[CHB][hapmap]
rs1886547	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs1924611	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1951922	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2004866	0.89[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2147363	0.82[CHD][hapmap]
rs2181891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274202	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs2277448	0.91[CHB][hapmap]
rs2296246	0.81[CEU][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs2296347	0.91[CHB][hapmap]
rs2296348	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2296349	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs2408544	0.89[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes]
rs2408550	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs2408551	0.82[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs2408552	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs2408554	0.91[CHB][hapmap]
rs2408609	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs2408611	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs2897964	0.91[CHB][hapmap]
rs2897977	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs3368	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs3742288	0.93[ASW][hapmap];0.96[CEU][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.85[LWK][hapmap];0.83[MEX][hapmap];0.88[MKK][hapmap];0.91[TSI][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3742289	0.91[CHB][hapmap]
rs3783241	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3783242	0.91[CHB][hapmap]
rs3818422	0.91[CHB][hapmap]
rs3825526	0.81[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs3825527	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]
rs3825528	0.89[CEU][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes]
rs4297592	0.85[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs4497567	0.91[CHB][hapmap]
rs4941727	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs6561656	0.91[CHB][hapmap]
rs723102	0.83[AMR][1000 genomes]
rs723103	0.83[AMR][1000 genomes]
rs732071	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7320831	0.91[CHB][hapmap]
rs7321120	0.91[CHB][hapmap]
rs7321435	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7324458	0.91[CHB][hapmap]
rs7327634	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes]
rs747781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs750290	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754610	0.81[CEU][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs755363	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs7981904	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs7991237	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs7994928	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7995946	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap]
rs7998770	0.91[CHB][hapmap]
rs7999812	0.96[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9316563	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526811	0.81[EUR][1000 genomes]
rs9526812	0.81[CEU][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs9526814	0.85[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs9526819	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9526821	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9526823	0.91[CHB][hapmap]
rs9526825	0.91[CHB][hapmap]
rs9526837	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs9526841	0.91[CHB][hapmap]
rs9526842	0.86[JPT][hapmap]
rs9535797	0.80[EUR][1000 genomes]
rs9535817	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535819	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535822	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535823	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535825	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9535826	0.89[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9535828	0.89[CEU][hapmap];1.00[MEX][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9535829	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9535832	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs9535833	0.88[AMR][1000 genomes]
rs9535836	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes]
rs9535851	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs9535856	0.81[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs9535858	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap]
rs9535861	0.82[CHB][hapmap]
rs9535862	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap]
rs9535866	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs9535867	0.91[CHB][hapmap]
rs9535873	0.91[CHB][hapmap]
rs9535878	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs9535879	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs9535880	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9535882	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9535885	0.86[JPT][hapmap]
rs9535887	0.81[CHB][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap]
rs9563084	0.88[AMR][1000 genomes]
rs9563089	0.89[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes]
rs9568677	0.81[CEU][hapmap];0.82[GIH][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs9568681	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568682	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs9568684	0.86[CHB][hapmap];0.89[JPT][hapmap]
rs9568713	0.85[CEU][hapmap];0.81[CHB][hapmap];0.85[GIH][hapmap];0.86[JPT][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9535812	CKAP2	cis	cerebellum	SCAN
rs9535812	LOC440138	cis	multi-tissue	Pritchard
rs9535812	CKAP2	cis	multi-tissue	Pritchard
rs9535812	ALG11	cis	Artery Tibial	GTEx
rs9535812	NCRNA00282	cis	cerebellum	SCAN
rs9535812	CKAP2	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:52513200-52553000	Weak transcription	Placenta	Placenta
4	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
5	chr13:52516600-52554000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr13:52516800-52555400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr13:52520600-52553000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:52525400-52553000	Weak transcription	Ovary	ovary
9	chr13:52529600-52553000	Weak transcription	Psoas Muscle	Psoas
10	chr13:52530200-52555400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr13:52530800-52553000	Weak transcription	Fetal Lung	lung
12	chr13:52532800-52553000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr13:52534400-52555400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr13:52537000-52552800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr13:52540000-52554600	Weak transcription	HSMMtube	muscle
16	chr13:52541000-52553000	Weak transcription	Left Ventricle	heart
17	chr13:52541400-52554800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr13:52541800-52553000	Weak transcription	Right Atrium	heart
19	chr13:52542400-52551400	Weak transcription	Lung	lung
20	chr13:52542800-52551000	Weak transcription	Fetal Muscle Leg	muscle
21	chr13:52544800-52554400	Weak transcription	Brain Anterior Caudate	brain
22	chr13:52544800-52556600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr13:52545000-52555400	Weak transcription	Adipose Nuclei	Adipose
24	chr13:52545000-52555600	Weak transcription	Aorta	Aorta
25	chr13:52545200-52552800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr13:52545400-52555400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr13:52546200-52553000	Weak transcription	Gastric	stomach
28	chr13:52546200-52553000	Weak transcription	Right Ventricle	heart
29	chr13:52546400-52552800	Weak transcription	Liver	Liver
30	chr13:52546400-52553000	Weak transcription	Pancreas	Pancrea
31	chr13:52548400-52552000	Weak transcription	Fetal Intestine Large	intestine
32	chr13:52548400-52552800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr13:52549000-52550800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr13:52549000-52555400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr13:52549000-52555600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr13:52549200-52551000	Weak transcription	Fetal Stomach	stomach
37	chr13:52549400-52551000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr13:52549400-52551600	Weak transcription	Fetal Intestine Small	intestine
39	chr13:52549800-52551800	Weak transcription	Fetal Heart	heart
40	chr13:52550000-52550800	Weak transcription	HepG2	liver
41	chr13:52550000-52553000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr13:52550200-52554200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr13:52550600-52550800	Genic enhancers	K562	blood

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