Variant report

Variant	rs17486
Chromosome Location	chr7:107112890-107112891
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	chr7:107109371..107111739-chr7:107112489..107114985,2	K562	blood:
2	chr7:107111916..107113727-chr7:107113763..107116184,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172209	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10464499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10464620	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953541	0.87[AFR][1000 genomes]
rs11532774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11766131	0.90[ASN][1000 genomes]
rs11770061	0.90[ASN][1000 genomes]
rs12056231	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12533694	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12534124	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12535038	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12535761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12539895	0.94[ASN][1000 genomes]
rs13234124	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17403088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17404067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17481621	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17481842	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17482494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17482543	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1978085	0.96[ASN][1000 genomes]
rs2283041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2299428	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2395880	0.90[ASN][1000 genomes]
rs2395881	0.90[ASN][1000 genomes]
rs34084719	0.96[ASN][1000 genomes]
rs34523267	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3779497	0.91[ASN][1000 genomes]
rs4515482	0.90[ASN][1000 genomes]
rs4727683	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4730248	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4730250	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56949084	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6945784	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6947674	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6955488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6957186	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6958969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6964395	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6976759	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6979198	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6979368	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs763386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7784906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7785085	0.91[AMR][1000 genomes]
rs7785962	0.87[AFR][1000 genomes]
rs7797791	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7801317	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7807154	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8180747	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825788	chr7:106897237-107136320	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1024793	chr7:106900877-107170312	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv1832266	chr7:106961882-107136320	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv1019963	chr7:107033342-107188641	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv539052	chr7:107033342-107188641	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17486	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107035800-107133000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr7:107052600-107126400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr7:107067600-107119800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr7:107083400-107115400	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:107088600-107126000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr7:107090000-107114600	Weak transcription	Primary T cells from cord blood	blood
7	chr7:107090800-107146000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:107091000-107145800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr7:107098800-107132600	Weak transcription	Primary B cells from cord blood	blood
10	chr7:107104200-107118000	Weak transcription	NHEK	skin
11	chr7:107104200-107121000	Weak transcription	K562	blood
12	chr7:107110200-107115400	Active TSS	Fetal Brain Male	brain
13	chr7:107110200-107117400	Active TSS	Fetal Brain Female	brain
14	chr7:107110400-107115600	Active TSS	Brain Cingulate Gyrus	brain
15	chr7:107110400-107115800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:107110800-107115400	Active TSS	Brain Angular Gyrus	brain
17	chr7:107110800-107115800	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr7:107111000-107115200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:107111800-107113000	Enhancers	HUVEC	blood vessel
20	chr7:107111800-107113000	Enhancers	NHLF	lung
21	chr7:107111800-107114000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:107111800-107115800	Active TSS	Right Atrium	heart
23	chr7:107112000-107114000	Enhancers	NHDF-Ad	bronchial
24	chr7:107112200-107113000	Enhancers	Fetal Lung	lung
25	chr7:107112200-107113200	Enhancers	Muscle Satellite Cultured Cells	--
26	chr7:107112200-107120800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr7:107112400-107113200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr7:107112600-107113000	Active TSS	Brain Substantia Nigra	brain
29	chr7:107112600-107113000	Active TSS	Left Ventricle	heart
30	chr7:107112600-107115800	Active TSS	Right Ventricle	heart
31	chr7:107112600-107116200	ZNF genes & repeats	Fetal Heart	heart
32	chr7:107112800-107113000	Enhancers	Brain Hippocampus Middle	brain
33	chr7:107112800-107113600	Weak transcription	Brain Anterior Caudate	brain
34	chr7:107112800-107145800	Weak transcription	Monocytes-CD14+_RO01746	blood

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