Variant report

Variant	rs9641378
Chromosome Location	chr7:106868003-106868004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:106867727..106869473-chr7:106870758..106873227,2	MCF-7	breast:
2	chr7:106860422..106863140-chr7:106865241..106868152,2	K562	blood:
3	chr7:106841256..106844464-chr7:106865963..106869229,3	K562	blood:
4	chr7:106867953..106869939-chr7:106873583..106876575,2	K562	blood:
5	chr7:106808669..106811412-chr7:106867096..106868996,2	K562	blood:

Variant related genes	Relation type
ENSG00000105856	Chromatin interaction

Extended variants
information (count: 156 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs1002935	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1018946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1018947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10253172	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs10253291	0.85[CEU][hapmap];0.89[AMR][1000 genomes]
rs10487271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10953529	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10953530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10953531	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10953533	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953534	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10953535	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10953537	0.95[ASN][1000 genomes]
rs1121312	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11761181	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11762152	0.83[ASN][1000 genomes]
rs11764448	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11766060	0.87[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11767623	0.83[AMR][1000 genomes]
rs11769527	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11769861	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11769901	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11773514	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12154285	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12531187	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12532447	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12532849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12532953	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12532967	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12533516	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12533767	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12534000	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12534676	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12535081	0.82[EUR][1000 genomes]
rs12535258	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12535814	0.93[ASN][1000 genomes]
rs12536485	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12536491	0.99[ASN][1000 genomes]
rs12536574	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12536603	0.96[ASN][1000 genomes]
rs12537011	0.95[ASN][1000 genomes]
rs12537374	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12537730	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537733	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12538090	0.81[EUR][1000 genomes]
rs12538769	0.82[EUR][1000 genomes]
rs12538848	0.82[EUR][1000 genomes]
rs12540475	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12705405	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs1548523	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1548524	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17349904	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17350182	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17427123	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17427158	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17427849	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17428071	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17428126	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17428504	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17429118	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17429146	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1981696	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs1989814	0.93[ASN][1000 genomes]
rs2023892	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2107318	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2107319	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189501	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2299422	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2395859	0.95[ASN][1000 genomes]
rs257371	0.83[AMR][1000 genomes]
rs257372	0.83[AMR][1000 genomes]
rs257373	0.83[AMR][1000 genomes]
rs257375	0.83[AMR][1000 genomes]
rs257377	0.84[CEU][hapmap];0.87[AMR][1000 genomes]
rs257378	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs257381	0.83[AMR][1000 genomes]
rs257382	0.83[AMR][1000 genomes]
rs257385	0.85[AMR][1000 genomes]
rs257386	0.85[AMR][1000 genomes]
rs257387	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs2894459	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3729876	0.84[CEU][hapmap];0.85[AMR][1000 genomes]
rs3729877	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs3757713	0.93[ASN][1000 genomes]
rs3779498	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3779500	0.84[CEU][hapmap];0.83[AMR][1000 genomes]
rs3801958	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3801959	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3801963	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3801965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3815148	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3823959	0.95[ASN][1000 genomes]
rs3823960	0.95[ASN][1000 genomes]
rs4727670	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4727671	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4730222	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4730223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4730224	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4730226	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4730227	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4730228	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4730229	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4730231	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4730232	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4730233	0.82[EUR][1000 genomes]
rs57525841	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58319984	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58663672	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59900773	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60255281	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61014091	0.83[ASN][1000 genomes]
rs61406169	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61511581	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61673847	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6466160	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs6466162	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6946036	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6946931	0.84[CEU][hapmap];0.85[AMR][1000 genomes]
rs6947675	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6947857	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs6949961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6951639	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6960148	0.85[CEU][hapmap];0.85[AMR][1000 genomes]
rs6960813	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6963917	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6964798	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6964966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6965001	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6967638	0.85[EUR][1000 genomes]
rs6967639	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6967745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6971675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6971774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6977868	0.82[CEU][hapmap];0.85[AMR][1000 genomes]
rs7777976	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7779062	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7781947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7783181	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7783562	0.96[ASN][1000 genomes]
rs7789500	0.91[ASN][1000 genomes]
rs7789678	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7793594	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7794598	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7794915	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7794965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7798223	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7800443	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7803290	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7807648	0.83[EUR][1000 genomes]
rs7981	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs997311	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	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
4	esv2756226	chr7:106850755-106944563	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9641378	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:106844000-106870400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr7:106844200-106873200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr7:106844600-106873600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr7:106844600-106880400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:106844600-106888400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:106846000-106925800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr7:106846200-106870600	Weak transcription	NH-A	brain
8	chr7:106849000-106873200	Weak transcription	Brain Anterior Caudate	brain
9	chr7:106849200-106872600	Weak transcription	HSMM	muscle
10	chr7:106850400-106890000	Weak transcription	Hela-S3	cervix
11	chr7:106850800-106869000	Weak transcription	NHEK	skin
12	chr7:106850800-106871000	Weak transcription	HMEC	breast
13	chr7:106850800-106895200	Weak transcription	Colon Smooth Muscle	Colon
14	chr7:106851000-106873600	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr7:106851000-106897600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr7:106851000-106946000	Weak transcription	Esophagus	oesophagus
17	chr7:106851200-106869200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr7:106851200-106869200	Weak transcription	Osteobl	bone
19	chr7:106851200-106873200	Weak transcription	Pancreas	Pancrea
20	chr7:106851200-106874800	Weak transcription	Ovary	ovary
21	chr7:106851200-106882200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr7:106851200-106888200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:106851200-106892400	Weak transcription	Gastric	stomach
24	chr7:106851200-106892600	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:106851400-106870600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr7:106851400-106873200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr7:106851600-106871400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:106853400-106925600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr7:106854400-106868400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr7:106854400-106878000	Weak transcription	K562	blood
31	chr7:106855200-106873600	Weak transcription	Right Ventricle	heart
32	chr7:106855600-106883000	Weak transcription	Dnd41	blood
33	chr7:106857200-106877000	Weak transcription	Primary hematopoietic stem cells	blood
34	chr7:106860200-106882600	Weak transcription	Fetal Muscle Trunk	muscle
35	chr7:106861400-106873200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr7:106861600-106876200	Weak transcription	Fetal Brain Female	brain
37	chr7:106863200-106869800	Strong transcription	Primary T cells from cord blood	blood
38	chr7:106863400-106869000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr7:106863400-106871200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr7:106863600-106874000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr7:106863800-106873200	Weak transcription	Psoas Muscle	Psoas
42	chr7:106863800-106873200	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr7:106863800-106887400	Weak transcription	Thymus	Thymus
44	chr7:106864000-106875800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr7:106864000-106878400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr7:106864000-106889600	Weak transcription	Spleen	Spleen
47	chr7:106864400-106871200	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr7:106864400-106871400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr7:106864600-106870400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr7:106865000-106887000	Weak transcription	Stomach Smooth Muscle	stomach

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