Variant report

Variant	rs4419417
Chromosome Location	chr3:121708355-121708356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:121707943..121710832-chr3:121713197..121716024,2	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11916150	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12695420	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13068522	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1474327	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1589700	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2091665	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2689276	0.82[AMR][1000 genomes]
rs2700424	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3817599	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6438689	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6770115	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6780559	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7626740	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7628167	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7638094	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7647751	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289184	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289185	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953730	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9815649	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9828757	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9829181	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9843053	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33139	chr3:121500400-122091831	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4419417	EAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121699000-121711200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:121699400-121714200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:121702600-121711600	Weak transcription	Fetal Intestine Small	intestine
4	chr3:121703000-121709000	Weak transcription	Fetal Intestine Large	intestine
5	chr3:121703200-121709000	Weak transcription	Primary B cells from cord blood	blood
6	chr3:121704200-121708800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr3:121704200-121709000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr3:121704800-121721400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:121705000-121711600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:121705200-121714000	Weak transcription	HMEC	breast
11	chr3:121705200-121729400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr3:121706000-121709000	Strong transcription	GM12878-XiMat	blood
13	chr3:121706000-121711600	Weak transcription	Esophagus	oesophagus
14	chr3:121706000-121721200	Weak transcription	Fetal Kidney	kidney
15	chr3:121706800-121708600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:121706800-121711600	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr3:121707000-121714200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:121707400-121708800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr3:121707400-121709200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:121707400-121711800	Weak transcription	Colonic Mucosa	Colon
21	chr3:121707600-121709000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:121707800-121710600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr3:121707800-121711400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr3:121708200-121708600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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