Variant report

Variant	rs34543553
Chromosome Location	chr3:121675637-121675638
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	chr3:121674203..121676977-chr3:121680188..121681967,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10934565	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488334	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488851	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491991	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12493408	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493952	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12496036	0.86[AMR][1000 genomes]
rs12497349	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12498028	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12629742	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12630486	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632345	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12637351	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637968	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12638492	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13067270	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13083557	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089878	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13093171	0.81[EUR][1000 genomes]
rs1344279	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1523519	0.84[AMR][1000 genomes]
rs1920290	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920291	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920297	0.83[EUR][1000 genomes]
rs1920298	0.84[EUR][1000 genomes]
rs1920299	0.84[EUR][1000 genomes]
rs1920309	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986368	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1986712	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2091664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293611	0.86[AMR][1000 genomes]
rs2332033	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2332035	0.91[EUR][1000 genomes]
rs2689285	0.84[EUR][1000 genomes]
rs2689290	0.84[EUR][1000 genomes]
rs2877560	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877561	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28823352	0.81[AMR][1000 genomes]
rs34158925	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34181646	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34478505	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34566912	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34696871	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34837785	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35101693	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35415993	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35737776	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35902163	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3915060	0.90[EUR][1000 genomes]
rs3942629	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4118376	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4285028	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4305455	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4676758	0.82[EUR][1000 genomes]
rs6790281	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71329246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71329247	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71329249	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73855465	0.84[EUR][1000 genomes]
rs73855476	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73855480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73855481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615571	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637495	0.84[EUR][1000 genomes]
rs7640872	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651226	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34543553	IQCB1	cis	Esophagus Muscularis	GTEx
rs34543553	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs34543553	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs34543553	ILDR1	Cis_1M	lymphoblastoid	RTeQTL
rs34543553	EAF2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121660200-121676600	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:121670400-121686800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:121671200-121676800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:121673200-121676000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr3:121673200-121676200	Weak transcription	Primary B cells from peripheral blood	blood
6	chr3:121673200-121676600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:121673400-121676600	Weak transcription	Primary B cells from cord blood	blood
8	chr3:121673400-121678800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:121674400-121676000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr3:121674800-121675800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:121674800-121675800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr3:121675000-121675800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:121675200-121675800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:121675200-121677400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr3:121675200-121678400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr3:121675400-121677200	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:121675600-121675800	Enhancers	Brain Anterior Caudate	brain
18	chr3:121675600-121676600	Weak transcription	GM12878-XiMat	blood

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