Variant report

Variant	rs4679654
Chromosome Location	chr3:160272388-160272389
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160272063..160274921-chr3:160279302..160283797,6	MCF-7	breast:
2	chr3:160271221..160273617-chr3:160281593..160283812,2	MCF-7	breast:
3	chr3:160270076..160273601-chr3:160274357..160279300,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229320	Chromatin interaction
ENSG00000186432	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1047210	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11706810	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11718121	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12632030	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1369666	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1451760	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1451764	0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs17236473	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17826221	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1920649	0.81[ASN][1000 genomes]
rs1920652	0.81[ASN][1000 genomes]
rs1920659	0.80[ASN][1000 genomes]
rs1971128	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2123003	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732706	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3851365	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4679888	0.80[AMR][1000 genomes]
rs4679890	0.84[AMR][1000 genomes]
rs4679895	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4679896	0.83[ASN][1000 genomes]
rs4680589	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680591	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55992947	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56156703	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62272792	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs62272794	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs62272800	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6785881	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6798668	0.84[AMR][1000 genomes]
rs6809153	0.80[AMR][1000 genomes]
rs7355951	0.80[AMR][1000 genomes]
rs7640072	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7648393	0.80[ASN][1000 genomes]
rs9816525	0.81[ASN][1000 genomes]
rs9822982	0.81[ASN][1000 genomes]
rs9857106	0.81[ASN][1000 genomes]

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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	nsv877701	chr3:160228001-160283815	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
8	nsv877702	chr3:160262803-160304614	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4679654	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160234600-160281000	Weak transcription	Aorta	Aorta
2	chr3:160240200-160280400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:160246600-160279200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:160247000-160281000	Weak transcription	Thymus	Thymus
5	chr3:160249200-160279000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:160251200-160282000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:160252800-160272600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:160254000-160272600	Weak transcription	Hela-S3	cervix
9	chr3:160254000-160279800	Weak transcription	Placenta	Placenta
10	chr3:160254200-160278800	Weak transcription	HMEC	breast
11	chr3:160258600-160273800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr3:160258800-160279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:160259200-160277000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:160259800-160272600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:160260200-160279600	Weak transcription	Osteobl	bone
16	chr3:160261800-160281000	Weak transcription	Ovary	ovary
17	chr3:160262000-160272400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:160262600-160277800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:160264000-160272600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:160264200-160282000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr3:160265200-160276800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr3:160265800-160272400	Weak transcription	Small Intestine	intestine
23	chr3:160266000-160272800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr3:160266400-160277400	Weak transcription	HUVEC	blood vessel
25	chr3:160266800-160272400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:160267200-160274600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr3:160268400-160273800	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:160268400-160279200	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr3:160268400-160281000	Weak transcription	Fetal Thymus	thymus
30	chr3:160268400-160281600	Weak transcription	Fetal Stomach	stomach
31	chr3:160268600-160275600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr3:160268800-160279800	Weak transcription	NHDF-Ad	bronchial
33	chr3:160269000-160279200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr3:160269000-160279400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr3:160269200-160281000	Weak transcription	Fetal Intestine Large	intestine
36	chr3:160269400-160272400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:160269400-160273800	Weak transcription	HSMM	muscle
38	chr3:160269400-160279200	Weak transcription	Dnd41	blood
39	chr3:160269400-160279200	Weak transcription	K562	blood
40	chr3:160269400-160281600	Weak transcription	Fetal Kidney	kidney
41	chr3:160269400-160281600	Weak transcription	Fetal Lung	lung
42	chr3:160269600-160273800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr3:160269600-160276000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:160269600-160278800	Weak transcription	NHEK	skin
45	chr3:160269600-160279200	Weak transcription	NH-A	brain
46	chr3:160269600-160279200	Weak transcription	NHLF	lung
47	chr3:160269800-160274000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:160269800-160279200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:160269800-160279600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:160270000-160277800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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