Variant report

Variant	rs1673612
Chromosome Location	chr3:138340728-138340729
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138334799..138337572-chr3:138340483..138342350,2	MCF-7	breast:

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10804658	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1082037	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1088055	0.94[AMR][1000 genomes]
rs13101081	0.92[AMR][1000 genomes]
rs1379257	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1479930	0.87[AMR][1000 genomes]
rs1600511	0.89[AMR][1000 genomes]
rs1672928	0.87[EUR][1000 genomes]
rs1672931	0.87[EUR][1000 genomes]
rs1672933	0.87[EUR][1000 genomes]
rs1672936	0.89[EUR][1000 genomes]
rs1672938	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1672939	0.87[AMR][1000 genomes]
rs1673593	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1673607	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1673624	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1679175	0.81[AMR][1000 genomes]
rs2348146	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2607795	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2881793	0.94[AMR][1000 genomes]
rs361073	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs361074	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs361075	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs361076	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs361077	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4432674	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4678264	0.86[AMR][1000 genomes]
rs484698	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs550507	0.94[AMR][1000 genomes]
rs559313	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs579750	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs586946	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs587005	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs587331	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60513493	0.82[AMR][1000 genomes]
rs609497	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs611134	0.92[AMR][1000 genomes]
rs61699523	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs618792	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs629884	0.93[AMR][1000 genomes]
rs634374	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs642258	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs654528	0.87[EUR][1000 genomes]
rs664928	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6798058	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs680070	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7625326	0.92[AMR][1000 genomes]
rs7627685	0.89[AMR][1000 genomes]
rs7634745	0.81[AMR][1000 genomes]
rs7643973	0.94[AMR][1000 genomes]
rs7653815	0.89[AMR][1000 genomes]
rs773444	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs773445	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs773448	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs773449	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs773452	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs773455	0.87[EUR][1000 genomes]
rs773456	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs811322	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs811793	0.81[AMR][1000 genomes]
rs9811052	0.89[AMR][1000 genomes]
rs9817419	0.94[AMR][1000 genomes]
rs9827256	0.92[AMR][1000 genomes]
rs9848718	0.90[AMR][1000 genomes]
rs9853998	0.90[AMR][1000 genomes]
rs9878436	0.93[AMR][1000 genomes];0.84[EUR][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	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1673612	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs1673612	FAIM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138328400-138350200	Weak transcription	Lung	lung
2	chr3:138328400-138353200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:138328400-138355000	Weak transcription	Esophagus	oesophagus
4	chr3:138328600-138346400	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:138328600-138349400	Weak transcription	Ovary	ovary
6	chr3:138328600-138358000	Weak transcription	Psoas Muscle	Psoas
7	chr3:138328800-138344800	Weak transcription	NHDF-Ad	bronchial
8	chr3:138328800-138358000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:138329000-138342200	Weak transcription	Fetal Stomach	stomach
10	chr3:138329000-138342800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:138329000-138344800	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:138329000-138346800	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:138329000-138347600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:138329000-138348000	Weak transcription	Fetal Intestine Large	intestine
15	chr3:138329000-138348200	Weak transcription	Left Ventricle	heart
16	chr3:138329000-138348400	Weak transcription	Aorta	Aorta
17	chr3:138329000-138348400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:138329000-138348600	Weak transcription	Fetal Intestine Small	intestine
19	chr3:138329000-138350000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:138329000-138354200	Weak transcription	Fetal Lung	lung
21	chr3:138329200-138342200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr3:138329200-138344600	Weak transcription	Osteobl	bone
23	chr3:138329200-138345000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:138329200-138348200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:138329600-138345600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:138330800-138342200	Weak transcription	Pancreas	Pancrea
27	chr3:138333200-138347000	Weak transcription	Fetal Thymus	thymus
28	chr3:138334200-138348600	Weak transcription	Thymus	Thymus
29	chr3:138334600-138345000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:138335400-138348200	Weak transcription	Adipose Nuclei	Adipose
31	chr3:138335400-138368000	Weak transcription	Right Ventricle	heart
32	chr3:138337000-138360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:138337800-138353600	Weak transcription	Colonic Mucosa	Colon
34	chr3:138338000-138353400	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:138338200-138346400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr3:138338200-138348200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr3:138338200-138350000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:138338600-138348000	Weak transcription	Hela-S3	cervix
39	chr3:138338600-138350400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr3:138339000-138348600	Weak transcription	Fetal Brain Female	brain
41	chr3:138339000-138351600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:138339400-138348000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:138339600-138344600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:138340400-138393800	Weak transcription	Fetal Brain Male	brain

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