Variant report

Variant	rs6446552
Chromosome Location	chr4:6924241-6924242
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:6910406..6912852-chr4:6922580..6925355,2	MCF-7	breast:
2	chr4:6918829..6920609-chr4:6923833..6926676,3	MCF-7	breast:
3	chr4:6922272..6924651-chr4:6925651..6927891,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132405	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10012305	0.87[ASN][1000 genomes]
rs10013211	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs10015163	1.00[JPT][hapmap]
rs10019900	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10804990	0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10937762	0.81[CHD][hapmap];0.95[JPT][hapmap]
rs10937763	0.89[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10937766	0.80[ASN][1000 genomes]
rs10937768	0.80[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10937770	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11723651	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11723719	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11728984	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11731639	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11732389	0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11732887	0.82[ASN][1000 genomes]
rs11733522	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11736355	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11930747	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11942739	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12499678	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12646620	0.80[ASN][1000 genomes]
rs12646621	0.80[ASN][1000 genomes]
rs13103361	0.80[ASN][1000 genomes]
rs13114976	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13149280	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13435015	0.85[JPT][hapmap]
rs17742611	0.86[JPT][hapmap]
rs2301820	0.86[JPT][hapmap]
rs28425595	0.81[ASN][1000 genomes]
rs28463777	0.80[ASN][1000 genomes]
rs28523495	0.80[ASN][1000 genomes]
rs28703753	0.87[ASN][1000 genomes]
rs3857170	0.82[JPT][hapmap]
rs41516949	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap]
rs4234787	0.87[ASN][1000 genomes]
rs4315786	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs4346651	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.91[YRI][hapmap]
rs4432749	0.90[JPT][hapmap]
rs4484301	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs4513567	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4608812	0.83[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4689055	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4689057	0.81[EUR][1000 genomes]
rs4689558	0.95[JPT][hapmap]
rs4689562	0.80[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs61488923	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62291136	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62292202	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6446550	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446551	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446553	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs6831368	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap]
rs6831590	0.83[ASN][1000 genomes]
rs6848114	0.94[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs7664348	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7668186	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7668673	0.89[CHB][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs7689337	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9291121	0.80[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs9291122	0.81[ASN][1000 genomes]
rs9291123	0.85[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs9291124	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9790586	0.89[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap]
rs9999025	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv878529	chr4:6883012-6983677	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription 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	30 gene(s)	inside rSNPs	diseases
2	nsv878530	chr4:6888932-7058473	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6446552	CPZ	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:6912600-6925400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:6913200-6925200	Weak transcription	NHLF	lung
3	chr4:6918600-6925000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr4:6918600-6925200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:6918600-6925200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr4:6918600-6925400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:6918800-6925000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:6918800-6925200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:6918800-6925200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr4:6918800-6925400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:6919000-6925200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr4:6919000-6925200	Weak transcription	NHEK	skin
13	chr4:6919000-6928000	Weak transcription	Fetal Kidney	kidney
14	chr4:6919200-6925400	Weak transcription	HSMMtube	muscle
15	chr4:6919600-6925200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr4:6919600-6925200	Weak transcription	Ovary	ovary
17	chr4:6919600-6925600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr4:6919600-6942200	Weak transcription	Hela-S3	cervix
19	chr4:6919800-6925000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:6920000-6925200	Weak transcription	Brain Angular Gyrus	brain
21	chr4:6920200-6925200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:6920200-6925200	Weak transcription	Colon Smooth Muscle	Colon
23	chr4:6920200-6925200	Weak transcription	Right Ventricle	heart
24	chr4:6920200-6925400	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr4:6920200-6927600	Weak transcription	Right Atrium	heart
26	chr4:6920200-6939600	Weak transcription	HUVEC	blood vessel
27	chr4:6920400-6925000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr4:6920400-6925000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:6920400-6925000	Weak transcription	Colonic Mucosa	Colon
30	chr4:6920400-6925000	Weak transcription	Dnd41	blood
31	chr4:6920400-6925200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr4:6920400-6925200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr4:6920400-6925200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr4:6920400-6925200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:6920400-6925200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr4:6920400-6925200	Weak transcription	Brain Cingulate Gyrus	brain
37	chr4:6920400-6925200	Weak transcription	Brain Germinal Matrix	brain
38	chr4:6920400-6925200	Weak transcription	Left Ventricle	heart
39	chr4:6920400-6925200	Weak transcription	A549	lung
40	chr4:6920400-6925400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr4:6920400-6925400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr4:6920400-6925400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:6920400-6925400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr4:6920400-6925400	Weak transcription	Pancreas	Pancrea
45	chr4:6920400-6925400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr4:6920400-6928600	Weak transcription	Psoas Muscle	Psoas
47	chr4:6920400-6931000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr4:6920600-6925000	Weak transcription	GM12878-XiMat	blood
49	chr4:6920600-6925200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr4:6920800-6924600	Weak transcription	Primary B cells from peripheral blood	blood

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