Variant report

Variant	rs4146689
Chromosome Location	chr10:22276819-22276820
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	chr10:22276606..22278159-chr10:22291193..22293980,2	K562	blood:

Variant related genes	Relation type
ENSG00000136770	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10508639	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10740997	0.83[TSI][hapmap]
rs10764328	0.89[MEX][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10764330	0.95[CEU][hapmap];0.93[GIH][hapmap]
rs10828266	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap]
rs10828283	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1086899	0.85[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs11012794	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap]
rs12571634	0.89[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2066270	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap]
rs2066271	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap]
rs2457954	0.83[CEU][hapmap]
rs2487512	0.85[CEU][hapmap]
rs2666750	0.85[CEU][hapmap]
rs2666754	1.00[ASW][hapmap];0.85[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2666757	1.00[ASW][hapmap];0.89[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2666759	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2666760	0.81[CEU][hapmap]
rs2666761	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2666768	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2666769	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs2666771	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap]
rs2666772	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2666775	1.00[CEU][hapmap];0.96[GIH][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2666776	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2666779	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap]
rs2666782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2807966	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2807967	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2807968	1.00[ASW][hapmap];0.84[CEU][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2807971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2807977	1.00[CHB][hapmap]
rs2807978	0.85[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs2807979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2807982	0.80[CEU][hapmap]
rs2807983	0.85[CEU][hapmap]
rs2807984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2807985	0.89[ASW][hapmap];0.95[CEU][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2807986	0.95[CEU][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2807987	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2807988	0.81[CEU][hapmap]
rs2859622	0.90[CEU][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2941732	0.80[EUR][1000 genomes]
rs2941733	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2986336	1.00[CHB][hapmap]
rs2998360	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2998361	0.83[AMR][1000 genomes]
rs4024198	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap]
rs4304660	1.00[YRI][hapmap]
rs4364959	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4748775	0.89[CEU][hapmap];0.87[ASN][1000 genomes]
rs4748776	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4748777	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4748778	0.86[AMR][1000 genomes]
rs4748779	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6482190	0.86[ASN][1000 genomes]
rs6650129	0.81[CEU][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs6650130	0.81[CEU][hapmap];0.88[EUR][1000 genomes]
rs7082663	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap]
rs7089656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs792453	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap];0.80[EUR][1000 genomes]
rs792454	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs792455	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs792456	0.84[CEU][hapmap]
rs806774	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1802317	chr10:21866085-22288132	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv1793816	chr10:22088054-22285371	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1048924	chr10:22177164-22296409	Enhancers Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv831808	chr10:22187850-22357814	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4146689	PXDN	trans	lymphoblastoid	seeQTL
rs4146689	PSTPIP2	trans	lymphoblastoid	seeQTL
rs4146689	MLLT10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22264600-22286000	Weak transcription	Gastric	stomach
2	chr10:22266000-22278400	Weak transcription	Pancreas	Pancrea
3	chr10:22266000-22282200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr10:22267600-22284400	Weak transcription	Osteobl	bone
5	chr10:22269600-22284000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr10:22275200-22278400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr10:22275600-22290000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:22275800-22278200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr10:22276600-22291000	Weak transcription	Brain Anterior Caudate	brain

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