Variant report

Variant	rs12535258
Chromosome Location	chr7:106971050-106971051
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	chr7:106970491..106972869-chr7:107219576..107221867,2	K562	blood:

Variant related genes	Relation type
ENSG00000272854	Chromatin interaction
ENSG00000075790	Chromatin interaction

Extended variants
information (count: 162 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:156)

rs_ID	r²[population]
rs1002935	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1018946	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs1018947	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10253172	0.85[CEU][hapmap]
rs10253291	0.85[CEU][hapmap]
rs10464620	0.94[CEU][hapmap]
rs10487271	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10953529	0.80[EUR][1000 genomes]
rs10953530	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10953531	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10953533	0.83[EUR][1000 genomes]
rs10953534	0.88[EUR][1000 genomes]
rs10953535	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10953536	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10953537	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1121312	0.88[EUR][1000 genomes]
rs11761181	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11764448	0.88[EUR][1000 genomes]
rs11766131	0.82[EUR][1000 genomes]
rs11769527	0.88[EUR][1000 genomes]
rs11769861	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11769901	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11770061	0.82[EUR][1000 genomes]
rs11773514	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12154285	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12155231	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531187	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12532447	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12532514	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12532849	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12532953	0.84[EUR][1000 genomes]
rs12532967	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12533516	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12533767	0.84[EUR][1000 genomes]
rs12534000	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12534676	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12535081	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535093	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12535814	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12536485	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12536491	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12536603	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12537011	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12537374	0.85[EUR][1000 genomes]
rs12537730	0.82[EUR][1000 genomes]
rs12537733	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12537785	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538090	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538769	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538848	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12540475	0.85[EUR][1000 genomes]
rs12705405	0.82[CEU][hapmap]
rs12705406	1.00[ASN][1000 genomes]
rs1548523	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1548524	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17349904	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17350182	0.87[EUR][1000 genomes]
rs17427123	0.82[EUR][1000 genomes]
rs17427158	0.81[EUR][1000 genomes]
rs17427849	0.84[EUR][1000 genomes]
rs17428071	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs17428126	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs17429118	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17429146	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17429825	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17481842	0.80[CEU][hapmap]
rs1981696	0.84[CEU][hapmap]
rs1989814	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2023892	0.84[EUR][1000 genomes]
rs2107318	0.84[EUR][1000 genomes]
rs2107319	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2189501	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2249043	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2299422	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2395859	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2395880	0.82[EUR][1000 genomes]
rs2395881	0.82[EUR][1000 genomes]
rs257377	0.84[CEU][hapmap]
rs257378	0.85[CEU][hapmap]
rs257387	0.84[CEU][hapmap]
rs2894459	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3729876	0.84[CEU][hapmap]
rs3729877	0.84[CEU][hapmap]
rs3757713	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3779498	0.88[EUR][1000 genomes]
rs3779500	0.84[CEU][hapmap]
rs3801958	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3801959	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3801963	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs3801965	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs3815148	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3823959	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3823960	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4515482	0.81[EUR][1000 genomes]
rs4727670	0.83[EUR][1000 genomes]
rs4727671	0.85[EUR][1000 genomes]
rs4730223	1.00[CEU][hapmap]
rs4730224	0.82[EUR][1000 genomes]
rs4730226	0.85[EUR][1000 genomes]
rs4730227	0.86[EUR][1000 genomes]
rs4730228	0.88[EUR][1000 genomes]
rs4730229	0.88[EUR][1000 genomes]
rs4730231	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4730232	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4730233	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730239	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730241	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730242	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730248	0.90[CEU][hapmap]
rs5002976	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57525841	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58319984	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58663672	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58689670	0.82[AMR][1000 genomes]
rs59782202	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59900773	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60255281	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61406169	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs61511581	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61673847	0.85[EUR][1000 genomes]
rs6466160	0.85[CEU][hapmap]
rs6466162	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6946036	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs6946931	0.84[CEU][hapmap]
rs6947675	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6947857	0.85[CEU][hapmap]
rs6949961	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6960148	0.85[CEU][hapmap]
rs6960813	0.89[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6963917	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6964798	0.88[EUR][1000 genomes]
rs6964966	0.88[EUR][1000 genomes]
rs6965001	0.88[EUR][1000 genomes]
rs6967639	0.82[EUR][1000 genomes]
rs6967745	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6971675	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6971774	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6977868	0.82[CEU][hapmap]
rs7777976	0.85[EUR][1000 genomes]
rs7779062	0.85[EUR][1000 genomes]
rs7781947	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs7783181	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7787027	0.80[YRI][hapmap]
rs7793594	0.85[EUR][1000 genomes]
rs7794598	1.00[CEU][hapmap]
rs7794965	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7798223	0.83[EUR][1000 genomes]
rs7800443	0.88[EUR][1000 genomes]
rs7803290	0.88[EUR][1000 genomes]
rs7804979	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807648	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7809508	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810216	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7981	0.94[CEU][hapmap];0.82[EUR][1000 genomes]
rs9641378	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs997311	0.94[AMR][1000 genomes];0.99[EUR][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	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
2	nsv888939	chr7:106849393-107045700	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv608073	chr7:106960515-107063686	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12535258	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106886400-106971400	Weak transcription	Fetal Muscle Trunk	muscle
2	chr7:106888800-106999400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr7:106923800-106999400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr7:106928000-106972600	Weak transcription	Fetal Muscle Leg	muscle
5	chr7:106934200-106971600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:106934200-106973000	Weak transcription	Adipose Nuclei	Adipose
7	chr7:106934400-106971400	Weak transcription	Ovary	ovary
8	chr7:106943000-106973000	Weak transcription	Thymus	Thymus
9	chr7:106945800-106973000	Weak transcription	Right Ventricle	heart
10	chr7:106946200-106999800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr7:106946400-106971400	Weak transcription	Esophagus	oesophagus
12	chr7:106946400-106973000	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr7:106946400-106978400	Weak transcription	Fetal Intestine Large	intestine
14	chr7:106946400-106983600	Weak transcription	Aorta	Aorta
15	chr7:106946400-106983600	Weak transcription	Fetal Intestine Small	intestine
16	chr7:106946400-106999400	Weak transcription	Pancreas	Pancrea
17	chr7:106948600-106973400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:106952400-106973600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr7:106953800-106999400	Weak transcription	Left Ventricle	heart
20	chr7:106954400-106971200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:106954600-106973000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr7:106955400-106973000	Weak transcription	Lung	lung
23	chr7:106959400-106973400	Weak transcription	NHDF-Ad	bronchial
24	chr7:106960000-106978200	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr7:106960400-106972400	Weak transcription	Psoas Muscle	Psoas
26	chr7:106960600-106974800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr7:106961200-106973000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr7:106961200-106973400	Weak transcription	Dnd41	blood
29	chr7:106961200-106982400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr7:106961400-106972400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr7:106963000-106972800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr7:106963000-106973200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr7:106963200-106971600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr7:106963200-106974000	Weak transcription	K562	blood
35	chr7:106963800-106972600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr7:106964200-106972800	Weak transcription	Primary B cells from cord blood	blood
37	chr7:106964200-106978400	Weak transcription	Liver	Liver
38	chr7:106964400-106971600	Weak transcription	HSMM	muscle
39	chr7:106964400-106972600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr7:106964400-106972600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr7:106964400-106973000	Weak transcription	Primary T helper cells fromperipheralblood	blood
42	chr7:106964400-106973000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr7:106964400-106977800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr7:106965400-106998000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr7:106967600-106978400	Weak transcription	Fetal Stomach	stomach
46	chr7:106967600-106983800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr7:106967800-106999800	Weak transcription	Fetal Heart	heart
48	chr7:106968400-106971800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr7:106968600-106972600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr7:106968800-106972000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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