Variant report

Variant	rs4943044
Chromosome Location	chr13:52517955-52517956
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:52515170..52518046-chr13:52524661..52527168,2	MCF-7	breast:
2	chr13:52516540..52519304-chr13:52583306..52585569,2	K562	blood:
3	chr13:52513900..52515674-chr13:52517334..52520081,2	K562	blood:

Variant related genes	Relation type
ENSG00000123191	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1051332	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1061472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.80[YRI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801249	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1924608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1924609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1924619	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1998611	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2031992	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.80[MEX][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2104353	0.95[CHB][hapmap];0.86[JPT][hapmap]
rs2282057	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2282058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2296246	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2408510	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3783240	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3825526	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs4943045	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943046	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7139967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7140038	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7321445	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7321909	0.84[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];0.95[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs732774	0.84[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];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328751	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs752569	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs754609	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs754610	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs928169	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316562	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs942463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9526812	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9526814	0.85[CHB][hapmap]
rs9535792	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535793	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535795	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9563078	0.81[JPT][hapmap]
rs9568677	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs9591439	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4943044	ATP7B	cis	cerebellum	SCAN
rs4943044	NEK5	cis	cerebellum	SCAN
rs4943044	CKAP2	cis	parietal	SCAN
rs4943044	THSD1	cis	cerebellum	SCAN
rs4943044	CKAP2	cis	cerebellum	SCAN
rs4943044	NCRNA00282	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52486400-52523400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr13:52492600-52539600	Weak transcription	Fetal Brain Male	brain
4	chr13:52494400-52558000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr13:52494800-52527000	Weak transcription	Fetal Lung	lung
6	chr13:52496600-52524200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr13:52497600-52519600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr13:52501000-52550400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr13:52501600-52532400	Strong transcription	HepG2	liver
10	chr13:52502800-52518000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr13:52502800-52529200	Weak transcription	Psoas Muscle	Psoas
12	chr13:52504200-52533600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr13:52504600-52537000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr13:52505600-52520800	Strong transcription	Fetal Intestine Small	intestine
15	chr13:52505600-52531800	Strong transcription	Liver	Liver
16	chr13:52505800-52527200	Strong transcription	Fetal Intestine Large	intestine
17	chr13:52506000-52520800	Strong transcription	Adipose Nuclei	Adipose
18	chr13:52506000-52527200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr13:52506800-52524400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr13:52507400-52518400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr13:52508000-52532200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:52509000-52518200	Weak transcription	Esophagus	oesophagus
23	chr13:52509000-52530000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:52509200-52549800	Weak transcription	Brain Substantia Nigra	brain
25	chr13:52509200-52553000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr13:52509400-52548600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr13:52509600-52518600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr13:52509800-52529600	Weak transcription	Small Intestine	intestine
29	chr13:52510000-52518600	Weak transcription	Spleen	Spleen
30	chr13:52511400-52520600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr13:52511400-52520600	Strong transcription	Right Ventricle	heart
32	chr13:52511800-52535800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:52512600-52544000	Weak transcription	Brain Angular Gyrus	brain
34	chr13:52512800-52518000	Weak transcription	Fetal Brain Female	brain
35	chr13:52513200-52518000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr13:52513200-52553000	Weak transcription	Placenta	Placenta
37	chr13:52513400-52542000	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr13:52513400-52555400	Weak transcription	Brain Hippocampus Middle	brain
39	chr13:52514600-52520600	Strong transcription	Stomach Smooth Muscle	stomach
40	chr13:52514600-52521000	Strong transcription	Fetal Muscle Leg	muscle
41	chr13:52514800-52518200	Strong transcription	Fetal Muscle Trunk	muscle
42	chr13:52514800-52518800	Strong transcription	Left Ventricle	heart
43	chr13:52514800-52519400	Strong transcription	HSMMtube	muscle
44	chr13:52514800-52520000	Strong transcription	Aorta	Aorta
45	chr13:52514800-52520800	Strong transcription	Brain Anterior Caudate	brain
46	chr13:52515400-52518000	Weak transcription	Lung	lung
47	chr13:52515400-52520600	Strong transcription	Brain Germinal Matrix	brain
48	chr13:52515600-52518800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr13:52515800-52520600	Strong transcription	Fetal Stomach	stomach
50	chr13:52515800-52520600	Strong transcription	Ovary	ovary

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