Variant report

Variant	rs17427123
Chromosome Location	chr7:106823661-106823662
allele	A/G
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	POLR2A	chr7:106823638-106823858	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:106548773..106551043-chr7:106822996..106824786,2	K562	blood:
2	chr7:106823314..106826111-chr7:107383213..107384790,2	K562	blood:
3	chr7:106823255..106826085-chr7:106831084..106833010,2	MCF-7	breast:

Variant related genes	Relation type
HBP1	TF binding region
ENSG00000105879	Chromatin interaction
ENSG00000241764	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs1002935	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1018946	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1018947	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10253172	0.91[AMR][1000 genomes]
rs10253291	0.83[AMR][1000 genomes]
rs10487271	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953529	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953530	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953531	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953533	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10953534	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10953535	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953537	0.93[ASN][1000 genomes]
rs1121312	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11761181	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11762152	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11764448	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11766060	0.92[ASN][1000 genomes]
rs11767623	0.89[AMR][1000 genomes]
rs11769527	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11769861	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11769901	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11773514	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12154285	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12531187	0.96[ASN][1000 genomes]
rs12532447	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12532849	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12532953	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532967	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12533516	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12533767	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12534000	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12534676	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12535081	0.80[EUR][1000 genomes]
rs12535258	0.82[EUR][1000 genomes]
rs12536485	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12536491	0.97[ASN][1000 genomes]
rs12536574	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12536603	0.95[ASN][1000 genomes]
rs12537011	0.93[ASN][1000 genomes]
rs12537374	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537730	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12537733	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12538769	0.81[EUR][1000 genomes]
rs12538848	0.81[EUR][1000 genomes]
rs12540475	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12705405	0.89[AMR][1000 genomes]
rs1548523	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1548524	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17349904	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17350182	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17427158	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17427849	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17428071	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17428126	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17428504	0.96[ASN][1000 genomes]
rs17429118	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17429146	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1981696	0.89[AMR][1000 genomes]
rs2023892	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2107318	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2107319	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2189501	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249043	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2299422	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2395859	0.93[ASN][1000 genomes]
rs257371	0.89[AMR][1000 genomes]
rs257372	0.89[AMR][1000 genomes]
rs257373	0.89[AMR][1000 genomes]
rs257375	0.89[AMR][1000 genomes]
rs257377	0.89[AMR][1000 genomes]
rs257378	0.91[AMR][1000 genomes]
rs257379	0.83[AMR][1000 genomes]
rs257381	0.89[AMR][1000 genomes]
rs257382	0.89[AMR][1000 genomes]
rs257385	0.91[AMR][1000 genomes]
rs257386	0.91[AMR][1000 genomes]
rs257387	0.89[AMR][1000 genomes]
rs2894459	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3729876	0.91[AMR][1000 genomes]
rs3729877	0.89[AMR][1000 genomes]
rs3779498	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3779500	0.89[AMR][1000 genomes]
rs3801958	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3801959	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3801963	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3801965	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815148	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3823959	0.93[ASN][1000 genomes]
rs3823960	0.93[ASN][1000 genomes]
rs4727670	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4727671	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730222	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4730223	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4730224	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4730226	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730227	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4730228	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4730229	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730231	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4730232	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4730233	0.81[EUR][1000 genomes]
rs57525841	0.96[ASN][1000 genomes]
rs58319984	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58663672	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59900773	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60255281	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61014091	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61406169	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61511581	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61673847	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6466160	0.89[AMR][1000 genomes]
rs6466162	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6946036	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6946931	0.91[AMR][1000 genomes]
rs6947675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6947857	0.91[AMR][1000 genomes]
rs6949961	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6951639	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6960148	0.91[AMR][1000 genomes]
rs6960813	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6963917	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6964798	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6964966	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6965001	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6967639	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6967745	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971675	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6971774	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977868	0.91[AMR][1000 genomes]
rs7777976	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7779062	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7781947	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7783181	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7783562	0.95[ASN][1000 genomes]
rs7789500	0.92[ASN][1000 genomes]
rs7789678	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7793594	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7794915	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7794965	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7798223	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7800443	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7803290	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7807648	0.82[EUR][1000 genomes]
rs7981	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9641378	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs997311	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831087	chr7:106673465-106872460	Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv3383027	chr7:106802625-107096474	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17427123	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106810600-106836800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr7:106810800-106826800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:106810800-106828200	Weak transcription	Esophagus	oesophagus
4	chr7:106810800-106836200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr7:106811000-106824200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr7:106811000-106826800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:106811000-106826800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr7:106811000-106828800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:106811400-106824800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr7:106811400-106825200	Weak transcription	Lung	lung
11	chr7:106811400-106825800	Weak transcription	NHLF	lung
12	chr7:106812200-106825200	Weak transcription	Aorta	Aorta
13	chr7:106812400-106826200	Weak transcription	Spleen	Spleen
14	chr7:106815200-106828200	Weak transcription	Pancreas	Pancrea
15	chr7:106815200-106849400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:106815800-106827800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr7:106816000-106843600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr7:106817400-106851400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr7:106819600-106851800	Strong transcription	Primary monocytes fromperipheralblood	blood
20	chr7:106819800-106846600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr7:106819800-106851600	Strong transcription	Dnd41	blood
22	chr7:106820000-106824800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr7:106820000-106851200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr7:106820000-106851600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr7:106820200-106825000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr7:106820200-106828600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:106820200-106828800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:106820200-106833600	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr7:106820200-106834600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr7:106820200-106837000	Weak transcription	Psoas Muscle	Psoas
31	chr7:106820200-106848400	Strong transcription	Placenta	Placenta
32	chr7:106820200-106851200	Strong transcription	Primary B cells from cord blood	blood
33	chr7:106820200-106851800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr7:106820200-106851800	Strong transcription	Fetal Thymus	thymus
35	chr7:106820400-106834000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr7:106820400-106834000	Strong transcription	Primary hematopoietic stem cells	blood
37	chr7:106820400-106845200	Strong transcription	HUES48 Cell Line	embryonic stem cell
38	chr7:106820400-106848200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr7:106820800-106825400	Weak transcription	Colonic Mucosa	Colon
40	chr7:106821000-106824400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr7:106821000-106826800	Weak transcription	Ovary	ovary
42	chr7:106821000-106828200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr7:106821000-106834200	Strong transcription	HepG2	liver
44	chr7:106821000-106840000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr7:106821000-106848400	Strong transcription	Liver	Liver
46	chr7:106821000-106854600	Strong transcription	Primary T cells from cord blood	blood
47	chr7:106821200-106825800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr7:106821200-106826200	Weak transcription	Right Ventricle	heart
49	chr7:106821200-106832600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:106821200-106834000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

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