Variant report

Variant	rs9591438
Chromosome Location	chr13:52498013-52498014
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52494041..52496295-chr13:52497772..52499467,2	MCF-7	breast:
2	chr13:52470122..52471057-chr13:52497836..52498780,6	K562	blood:
3	chr13:52484875..52491698-chr13:52491732..52499779,14	MCF-7	breast:
4	chr13:52496037..52498400-chr13:52502438..52504247,2	K562	blood:
5	chr13:52416388..52418055-chr13:52496195..52498619,2	K562	blood:
6	chr13:52496511..52499468-chr13:52568718..52570837,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1051332	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs1061472	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs1801244	0.83[MEX][hapmap]
rs1801249	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs1924608	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs1924609	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs1998611	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs2031992	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2104353	0.90[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2282058	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs2296246	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs3742288	0.83[MEX][hapmap]
rs3783240	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs3825526	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs3825527	0.84[MEX][hapmap]
rs4943040	0.85[CEU][hapmap]
rs4943044	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4943045	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4943046	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4943048	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs7139967	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs7321445	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs7321909	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs732774	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs7328751	0.85[CEU][hapmap];0.83[ASN][1000 genomes]
rs752569	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs752570	0.86[ASN][1000 genomes]
rs754610	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs942463	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs9526811	0.88[ASN][1000 genomes]
rs9526812	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9526814	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs9535796	0.95[CHB][hapmap]
rs9535797	0.89[ASN][1000 genomes]
rs9563078	0.87[ASN][1000 genomes]
rs9568677	0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs9591439	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]

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	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	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer 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	27 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9591438	ATP7B	cis	cerebellum	SCAN
rs9591438	CKAP2	cis	parietal	SCAN
rs9591438	CKAP2	cis	cerebellum	SCAN
rs9591438	NCRNA00282	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52481600-52502000	Weak transcription	Right Atrium	heart
2	chr13:52481800-52506000	Weak transcription	Ovary	ovary
3	chr13:52486400-52500200	Weak transcription	Fetal Kidney	kidney
4	chr13:52486400-52523400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:52486800-52502000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr13:52487000-52507800	Weak transcription	Pancreas	Pancrea
7	chr13:52488000-52507800	Weak transcription	Brain Anterior Caudate	brain
8	chr13:52488000-52508200	Weak transcription	Brain Angular Gyrus	brain
9	chr13:52488000-52508200	Weak transcription	Brain Hippocampus Middle	brain
10	chr13:52488200-52505800	Weak transcription	Brain Germinal Matrix	brain
11	chr13:52488200-52508000	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr13:52489600-52508400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr13:52490000-52509400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr13:52491200-52499800	Weak transcription	Fetal Heart	heart
16	chr13:52491200-52500200	Weak transcription	Lung	lung
17	chr13:52492000-52508400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr13:52492600-52539600	Weak transcription	Fetal Brain Male	brain
19	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr13:52494600-52500000	Weak transcription	Gastric	stomach
21	chr13:52494800-52527000	Weak transcription	Fetal Lung	lung
22	chr13:52495000-52500800	Strong transcription	Fetal Intestine Small	intestine
23	chr13:52495400-52512600	Weak transcription	Colon Smooth Muscle	Colon
24	chr13:52495600-52501800	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr13:52495600-52508200	Weak transcription	Brain Substantia Nigra	brain
26	chr13:52495600-52515000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr13:52496200-52498400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr13:52496200-52508200	Weak transcription	Stomach Mucosa	stomach
29	chr13:52496200-52508200	Weak transcription	Spleen	Spleen
30	chr13:52496400-52498200	Enhancers	Fetal Thymus	thymus
31	chr13:52496400-52499400	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr13:52496600-52498200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr13:52496600-52498400	Weak transcription	Placenta	Placenta
34	chr13:52496600-52499600	Weak transcription	HSMMtube	muscle
35	chr13:52496600-52500600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr13:52496600-52507200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr13:52496600-52524200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr13:52496800-52498800	Strong transcription	Fetal Muscle Leg	muscle
39	chr13:52497200-52501400	Weak transcription	Left Ventricle	heart
40	chr13:52497400-52508400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr13:52497600-52498200	Weak transcription	HepG2	liver
42	chr13:52497600-52499800	Weak transcription	Duodenum Mucosa	Duodenum
43	chr13:52497600-52501400	Enhancers	K562	blood
44	chr13:52497600-52501800	Weak transcription	Fetal Stomach	stomach
45	chr13:52497600-52505800	Weak transcription	Aorta	Aorta
46	chr13:52497600-52505800	Weak transcription	Fetal Intestine Large	intestine
47	chr13:52497600-52507800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr13:52497600-52508000	Weak transcription	Fetal Brain Female	brain
49	chr13:52497600-52508800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr13:52497600-52519600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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