Variant report

Variant	rs669371
Chromosome Location	chr11:65674153-65674154
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65655695..65656411-chr11:65673994..65674721,2	K562	blood:

Variant related genes	Relation type
ENSG00000172500	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10160792	0.90[EUR][1000 genomes]
rs1058068	0.95[EUR][1000 genomes]
rs1151523	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12361552	0.82[CEU][hapmap]
rs526631	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs552130	0.85[GIH][hapmap]
rs556872	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs589253	0.87[GIH][hapmap];0.85[MEX][hapmap]
rs590318	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs590871	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593525	0.85[GIH][hapmap]
rs617791	0.82[CEU][hapmap];0.95[GIH][hapmap]
rs61893932	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs624273	0.86[CHD][hapmap];0.85[GIH][hapmap]
rs634534	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs637571	0.85[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs653914	0.89[CEU][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs674363	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs677029	0.89[CEU][hapmap];0.89[GIH][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs688862	0.83[CHD][hapmap];0.85[GIH][hapmap]
rs689274	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs694156	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897736	chr11:65335705-65676516	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	227 gene(s)	inside rSNPs	diseases
2	nsv430401	chr11:65419324-65788024	Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	224 gene(s)	inside rSNPs	diseases
3	esv2758274	chr11:65559893-65722363	Genic enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	esv2759834	chr11:65559893-65722363	Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv427890	chr11:65559893-65722363	Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
6	nsv897761	chr11:65580638-65738566	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	186 gene(s)	inside rSNPs	diseases
7	nsv555215	chr11:65581579-65676516	Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
8	nsv897762	chr11:65613218-65758854	Active TSS Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	185 gene(s)	inside rSNPs	diseases
9	nsv897764	chr11:65613348-65695222	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
10	nsv897765	chr11:65623708-65758854	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
11	nsv832191	chr11:65632329-65806120	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs669371	PRDX5	cis	cerebellum	SCAN
rs669371	PACS1	cis	parietal	SCAN
rs669371	RAB1B	cis	cerebellum	SCAN
rs669371	PCNXL3	cis	parietal	SCAN
rs669371	SART1	cis	parietal	SCAN
rs669371	EIF1AD	cis	parietal	SCAN
rs669371	EFEMP2	cis	cerebellum	SCAN
rs669371	KCNK4	cis	cerebellum	SCAN
rs669371	SNX32	cis	cerebellum	SCAN
rs669371	CARNS1	cis	cerebellum	SCAN
rs669371	TSGA10IP	cis	cerebellum	SCAN
rs669371	SNX32	cis	parietal	SCAN
rs669371	FADS3	cis	parietal	SCAN
rs669371	LRRN4CL	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65668000-65682600	Weak transcription	Aorta	Aorta
2	chr11:65671200-65678800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:65671200-65679000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:65671200-65679400	Weak transcription	HSMMtube	muscle
5	chr11:65671400-65674200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr11:65671400-65674200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:65671400-65676600	Weak transcription	Fetal Thymus	thymus
8	chr11:65671600-65674200	Weak transcription	HMEC	breast
9	chr11:65671600-65676400	Weak transcription	HepG2	liver
10	chr11:65671600-65676600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:65671600-65677600	Weak transcription	NHLF	lung
12	chr11:65671600-65678600	Weak transcription	NH-A	brain
13	chr11:65671800-65674200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:65671800-65674200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr11:65671800-65674200	Weak transcription	NHDF-Ad	bronchial
16	chr11:65671800-65676600	Weak transcription	Hela-S3	cervix
17	chr11:65671800-65677600	Weak transcription	A549	lung
18	chr11:65672000-65677000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr11:65672000-65678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr11:65672600-65678800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:65672800-65677800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:65673400-65678000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr11:65674000-65674600	Enhancers	HSMM	muscle
24	chr11:65674000-65674800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr11:65674000-65674800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:65674000-65674800	Flanking Active TSS	K562	blood
27	chr11:65674000-65674800	Enhancers	NHEK	skin
28	chr11:65674000-65674800	Enhancers	Osteobl	bone
29	chr11:65674000-65675000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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