Variant report

Variant	rs8180747
Chromosome Location	chr7:107106308-107106309
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr7:107106214-107106579	SH-SY5Y	brain:	n/a	chr7:107106331-107106338

No.	Distal block	Cell Line	Cell type
1	chr7:107105274..107109720-chr7:107110378..107116920,7	K562	blood:
2	chr7:107106073..107108563-chr7:107381011..107383684,2	K562	blood:
3	chr7:107105733..107108568-chr7:107114784..107116920,2	K562	blood:
4	chr7:107103654..107106333-chr7:107361202..107363848,2	MCF-7	breast:

Variant related genes	Relation type
GPR22	TF binding region
ENSG00000172209	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10464499	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10464620	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10953541	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs11532774	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11766131	0.89[ASN][1000 genomes]
rs11770061	0.89[ASN][1000 genomes]
rs12056231	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12532447	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12532849	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12533694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12534124	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12535038	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12535761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12539895	0.93[ASN][1000 genomes]
rs13234124	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17403088	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17404067	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17481621	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17481842	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17482494	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17482543	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17486	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1978085	0.97[ASN][1000 genomes]
rs2249043	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2283041	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299428	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2395880	0.89[ASN][1000 genomes]
rs2395881	0.89[ASN][1000 genomes]
rs2894459	0.83[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs34084719	0.97[ASN][1000 genomes]
rs34523267	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3779497	0.90[ASN][1000 genomes]
rs4515482	0.89[ASN][1000 genomes]
rs4727683	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4730248	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56949084	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6945784	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6947674	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6955488	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6957186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6958969	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6964395	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6964966	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6976759	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6979198	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6979368	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs763386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7784906	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7785085	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7785962	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes]
rs7797791	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7801317	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7807154	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[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
rs8180747	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 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	chr7:107079600-107108600	Weak transcription	Right Ventricle	heart
5	chr7:107082800-107109000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr7:107083400-107115400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:107084400-107109200	Weak transcription	Fetal Intestine Large	intestine
8	chr7:107087800-107112000	Weak transcription	NHDF-Ad	bronchial
9	chr7:107088600-107126000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr7:107090000-107114600	Weak transcription	Primary T cells from cord blood	blood
11	chr7:107090800-107146000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:107091000-107145800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr7:107097000-107112200	Weak transcription	Fetal Lung	lung
14	chr7:107098000-107108000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr7:107098800-107132600	Weak transcription	Primary B cells from cord blood	blood
16	chr7:107099600-107110400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr7:107103600-107110000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr7:107103800-107109800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr7:107104200-107118000	Weak transcription	NHEK	skin
20	chr7:107104200-107121000	Weak transcription	K562	blood
21	chr7:107104400-107109800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr7:107104400-107110400	Weak transcription	Left Ventricle	heart
23	chr7:107104400-107112400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:107104600-107110000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr7:107105200-107110600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr7:107105400-107110200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr7:107105600-107106600	Weak transcription	Fetal Heart	heart
28	chr7:107105600-107108600	Weak transcription	Brain Anterior Caudate	brain
29	chr7:107105600-107108600	Weak transcription	Brain Hippocampus Middle	brain
30	chr7:107105600-107109800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr7:107105600-107110000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr7:107105600-107110000	Weak transcription	Brain Angular Gyrus	brain
33	chr7:107105600-107110400	Weak transcription	Brain Substantia Nigra	brain

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