Variant report

Variant	rs2998360
Chromosome Location	chr10:22246114-22246115
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:22244305..22247068-chr10:22628599..22631062,2	K562	blood:
2	chr10:22238836..22240855-chr10:22243838..22246285,2	K562	blood:

Variant related genes	Relation type
ENSG00000272366	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10508639	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[EUR][1000 genomes]
rs10740991	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs10764328	0.83[GIH][hapmap];0.89[MEX][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10764330	0.89[CEU][hapmap]
rs10828266	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[MEX][hapmap]
rs10828283	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1086899	0.80[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs11012794	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs11012837	1.00[JPT][hapmap]
rs12571634	0.89[ASW][hapmap];0.95[CEU][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2066270	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs2066271	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs2487512	0.80[CEU][hapmap]
rs2666750	0.80[CEU][hapmap]
rs2666754	1.00[ASW][hapmap];0.90[CEU][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2666756	0.81[CEU][hapmap]
rs2666757	1.00[ASW][hapmap];0.94[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2666759	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2666761	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2666768	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2666769	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes]
rs2666771	0.89[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap]
rs2666772	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2666775	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs2666776	1.00[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2666779	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];0.86[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes]
rs2666782	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2793353	0.81[AMR][1000 genomes]
rs2807966	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2807967	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2807968	1.00[ASW][hapmap];0.89[CEU][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2807971	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[EUR][1000 genomes]
rs2807977	1.00[CHB][hapmap]
rs2807978	0.80[CEU][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs2807979	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2807983	0.80[CEU][hapmap]
rs2807984	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2807985	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];0.97[TSI][hapmap];0.88[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2807986	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2807987	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2859622	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2941732	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2941733	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2986336	1.00[CHB][hapmap]
rs2998361	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3951780	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];0.84[TSI][hapmap]
rs4024198	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs4146689	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]
rs4304660	0.88[YRI][hapmap]
rs4364959	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4748775	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs4748776	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4748777	0.93[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4748778	0.82[AMR][1000 genomes]
rs4748779	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6650129	0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs6650130	0.88[EUR][1000 genomes]
rs7082663	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap]
rs7089656	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7910002	0.80[CEU][hapmap]
rs792453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs792454	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs792455	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs792456	0.89[CEU][hapmap];0.94[GIH][hapmap]
rs806774	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
5	nsv894948	chr10:22203392-22255097	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1795981	chr10:22223984-22253054	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv894949	chr10:22241988-22264558	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2998360	PXDN	trans	lymphoblastoid	seeQTL
rs2998360	MLLT10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22199600-22250800	Weak transcription	Pancreas	Pancrea
2	chr10:22237200-22250800	Weak transcription	Left Ventricle	heart
3	chr10:22238200-22250400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr10:22244000-22250800	Weak transcription	Right Ventricle	heart
5	chr10:22244400-22247400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr10:22245000-22247000	Enhancers	Fetal Heart	heart
7	chr10:22245200-22251400	Weak transcription	Psoas Muscle	Psoas
8	chr10:22245400-22248800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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