Variant report

Variant	rs17482543
Chromosome Location	chr7:107169174-107169175
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107164671..107167823-chr7:107168530..107171856,3	K562	blood:
2	chr7:107165019..107167823-chr7:107168530..107171856,3	K562	blood:
3	chr7:107166785..107169332-chr7:107203065..107207052,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164597	Chromatin interaction
ENSG00000105865	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10464499	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10464620	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11532774	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11766131	0.88[ASN][1000 genomes]
rs11770061	0.88[ASN][1000 genomes]
rs12056231	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12533694	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12534124	0.99[ASN][1000 genomes]
rs12535038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12535761	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12539895	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13234124	0.89[ASN][1000 genomes]
rs17403088	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17404067	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17481621	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17481842	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17482494	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17486	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1978085	0.93[ASN][1000 genomes]
rs2283041	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2299428	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2395880	0.88[ASN][1000 genomes]
rs2395881	0.88[ASN][1000 genomes]
rs34084719	0.93[ASN][1000 genomes]
rs34523267	0.89[ASN][1000 genomes]
rs3779497	0.89[ASN][1000 genomes]
rs4515482	0.88[ASN][1000 genomes]
rs4727683	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4730248	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4730250	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56949084	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6945784	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6947674	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6955488	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957186	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6958969	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6964395	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6976759	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6979198	0.92[ASN][1000 genomes]
rs6979368	0.92[ASN][1000 genomes]
rs763386	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7784906	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7785085	0.91[AMR][1000 genomes]
rs7797791	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7801317	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7807154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180747	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv1028571	chr7:107114479-107299723	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv539053	chr7:107114479-107299723	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv482365	chr7:107122401-107271861	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17482543	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107126800-107184800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr7:107127400-107175400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr7:107131400-107179800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr7:107131800-107175000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr7:107144800-107185000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr7:107146000-107185000	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:107146400-107183800	Weak transcription	Ovary	ovary
8	chr7:107146400-107183800	Weak transcription	Thymus	Thymus
9	chr7:107146400-107184000	Weak transcription	Aorta	Aorta
10	chr7:107147000-107169800	Weak transcription	Gastric	stomach
11	chr7:107147000-107178200	Weak transcription	Liver	Liver
12	chr7:107147600-107169600	Weak transcription	Pancreas	Pancrea
13	chr7:107147600-107178400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr7:107147600-107183600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:107149400-107183800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr7:107149600-107178800	Weak transcription	Fetal Stomach	stomach
17	chr7:107153800-107183800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr7:107154000-107193800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr7:107155200-107171200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:107156000-107178400	Weak transcription	Fetal Intestine Large	intestine
21	chr7:107156400-107195000	Weak transcription	Colon Smooth Muscle	Colon
22	chr7:107157400-107169600	Weak transcription	Fetal Heart	heart
23	chr7:107157600-107169600	Weak transcription	Left Ventricle	heart
24	chr7:107158000-107183800	Weak transcription	Esophagus	oesophagus
25	chr7:107159400-107172400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr7:107160200-107169200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr7:107161000-107185000	Weak transcription	HSMMtube	muscle
28	chr7:107161600-107169200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr7:107162000-107169200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr7:107162000-107178600	Weak transcription	Lung	lung
31	chr7:107162000-107184000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr7:107162200-107203400	Weak transcription	Fetal Kidney	kidney
33	chr7:107162600-107177400	Weak transcription	Fetal Muscle Leg	muscle
34	chr7:107162800-107177800	Weak transcription	Primary B cells from cord blood	blood
35	chr7:107163000-107184400	Weak transcription	Colonic Mucosa	Colon
36	chr7:107163200-107184600	Weak transcription	NHLF	lung
37	chr7:107163400-107178400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr7:107163400-107184200	Weak transcription	Fetal Thymus	thymus
39	chr7:107163600-107184800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr7:107163800-107169800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr7:107164200-107185800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr7:107164400-107170800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr7:107164600-107182800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr7:107164800-107185000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr7:107166400-107169600	Weak transcription	Fetal Intestine Small	intestine
46	chr7:107166400-107169800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr7:107166600-107194600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr7:107166800-107172400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr7:107167000-107172200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr7:107167000-107184400	Weak transcription	Placenta	Placenta

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