Variant report

Variant	rs34478505
Chromosome Location	chr3:121694071-121694072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10934565	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488334	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488851	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491991	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12493408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493952	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12496036	0.82[AMR][1000 genomes]
rs12497349	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12498028	0.84[EUR][1000 genomes]
rs12629742	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12630486	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12632345	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12637351	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12637968	0.84[EUR][1000 genomes]
rs12638492	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13067270	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13083557	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089878	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13093171	0.81[EUR][1000 genomes]
rs1344279	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1523519	0.84[AMR][1000 genomes]
rs1920290	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920291	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920297	0.82[EUR][1000 genomes]
rs1920298	0.84[EUR][1000 genomes]
rs1920299	0.84[EUR][1000 genomes]
rs1920309	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986368	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1986712	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2091664	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2293611	0.82[AMR][1000 genomes]
rs2332033	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2332035	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2689285	0.83[EUR][1000 genomes]
rs2689290	0.83[EUR][1000 genomes]
rs2877560	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2877561	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34158925	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34181646	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34543553	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34566912	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34696871	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34837785	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35101693	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35415993	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35737776	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35902163	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3915060	0.89[EUR][1000 genomes]
rs3942629	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4118376	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4285028	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4305455	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4676758	0.81[EUR][1000 genomes]
rs6790281	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71329246	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71329247	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71329249	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73855465	0.83[EUR][1000 genomes]
rs73855476	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73855480	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73855481	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615571	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637495	0.83[EUR][1000 genomes]
rs7640872	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651226	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[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
rs34478505	IQCB1	cis	Esophagus Muscularis	GTEx
rs34478505	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs34478505	ILDR1	Cis_1M	lymphoblastoid	RTeQTL
rs34478505	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs34478505	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121686000-121698200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr3:121690000-121694800	Weak transcription	Pancreas	Pancrea
3	chr3:121691200-121695600	Enhancers	HMEC	breast
4	chr3:121692200-121695400	Enhancers	NHEK	skin
5	chr3:121693000-121694200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:121693200-121695200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:121693600-121694200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr3:121693800-121694800	Weak transcription	Primary B cells from cord blood	blood
9	chr3:121693800-121695200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:121694000-121695200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr3:121694000-121697200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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