Variant report

Variant	rs2886825
Chromosome Location	chr3:160273537-160273538
allele	C/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	chr3:160272617..160274929-chr3:160276167..160279036,2	MCF-7	breast:
3	chr3:160271221..160273617-chr3:160281593..160283812,2	MCF-7	breast:
4	chr3:160167702..160169385-chr3:160272825..160274892,2	K562	blood:
5	chr3:160254211..160257700-chr3:160273142..160275155,4	MCF-7	breast:
6	chr3:160270076..160273601-chr3:160274357..160279300,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186432	Chromatin interaction
ENSG00000229320	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10212236	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1317365	0.85[EUR][1000 genomes]
rs13403	0.85[ASN][1000 genomes]
rs1451761	0.80[AMR][1000 genomes]
rs1451762	0.80[AMR][1000 genomes]
rs1451764	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1551190	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1584688	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236544	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17570467	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1882126	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1882127	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920642	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1920662	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1920664	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2152425	0.81[AMR][1000 genomes]
rs2279457	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2305407	0.80[AMR][1000 genomes]
rs2366969	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28705750	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3732707	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3773372	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4091703	0.91[ASN][1000 genomes]
rs41272947	0.88[AMR][1000 genomes]
rs4292273	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4292274	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4621370	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679655	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4679885	0.85[ASN][1000 genomes]
rs4679888	0.87[EUR][1000 genomes]
rs4679889	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4679890	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679891	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679896	0.80[EUR][1000 genomes]
rs4679899	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4679900	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4680585	0.88[ASN][1000 genomes]
rs4680587	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4680588	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56156703	0.82[ASN][1000 genomes]
rs56197102	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58322641	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60460891	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62272791	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62272792	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62272794	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272800	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62272810	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6441319	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6441320	0.86[ASN][1000 genomes]
rs6441324	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6768975	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6793560	0.80[AMR][1000 genomes]
rs6798668	0.86[EUR][1000 genomes]
rs6801300	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6806505	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs721022	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs721023	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7356111	0.86[AMR][1000 genomes]
rs7618974	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7621724	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627749	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7627756	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7629	0.85[ASN][1000 genomes]
rs7629202	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7631792	0.82[ASN][1000 genomes]
rs7632307	0.81[AMR][1000 genomes]
rs7634108	0.80[AMR][1000 genomes]
rs7634826	0.80[AMR][1000 genomes]
rs7640072	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7643779	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644453	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7645832	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7647873	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862595	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9968151	0.80[AMR][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
rs2886825	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	chr3:160254000-160279800	Weak transcription	Placenta	Placenta
8	chr3:160254200-160278800	Weak transcription	HMEC	breast
9	chr3:160258600-160273800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:160258800-160279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:160259200-160277000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:160260200-160279600	Weak transcription	Osteobl	bone
13	chr3:160261800-160281000	Weak transcription	Ovary	ovary
14	chr3:160262600-160277800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr3:160264200-160282000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:160265200-160276800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:160266400-160277400	Weak transcription	HUVEC	blood vessel
18	chr3:160267200-160274600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:160268400-160273800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:160268400-160279200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr3:160268400-160281000	Weak transcription	Fetal Thymus	thymus
22	chr3:160268400-160281600	Weak transcription	Fetal Stomach	stomach
23	chr3:160268600-160275600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr3:160268800-160279800	Weak transcription	NHDF-Ad	bronchial
25	chr3:160269000-160279200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:160269000-160279400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr3:160269200-160281000	Weak transcription	Fetal Intestine Large	intestine
28	chr3:160269400-160273800	Weak transcription	HSMM	muscle
29	chr3:160269400-160279200	Weak transcription	Dnd41	blood
30	chr3:160269400-160279200	Weak transcription	K562	blood
31	chr3:160269400-160281600	Weak transcription	Fetal Kidney	kidney
32	chr3:160269400-160281600	Weak transcription	Fetal Lung	lung
33	chr3:160269600-160273800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr3:160269600-160276000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:160269600-160278800	Weak transcription	NHEK	skin
36	chr3:160269600-160279200	Weak transcription	NH-A	brain
37	chr3:160269600-160279200	Weak transcription	NHLF	lung
38	chr3:160269800-160274000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:160269800-160279200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr3:160269800-160279600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:160270000-160277800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:160270000-160281800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:160270200-160282000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:160270400-160277400	Weak transcription	Primary B cells from cord blood	blood
45	chr3:160270400-160280800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:160271200-160276800	Weak transcription	Primary T cells from cord blood	blood
47	chr3:160271200-160279200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr3:160271400-160276600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr3:160271400-160281000	Weak transcription	Fetal Muscle Leg	muscle
50	chr3:160271600-160276800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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