Variant report

Variant	rs12056231
Chromosome Location	chr7:107186093-107186094
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	chr7:107178929..107181687-chr7:107183616..107186437,2	K562	blood:
2	chr7:107183753..107186619-chr7:107203811..107206645,3	K562	blood:

Variant related genes	Relation type
ENSG00000105865	Chromatin interaction
ENSG00000164597	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	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10464620	0.93[ASN][1000 genomes]
rs11532774	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11766131	0.86[ASN][1000 genomes]
rs11770061	0.86[ASN][1000 genomes]
rs12533694	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12534124	0.92[ASN][1000 genomes]
rs12535038	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12535761	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12539895	0.92[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs13234124	0.93[ASN][1000 genomes]
rs17403088	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17404067	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17481621	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17481842	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17482494	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17482543	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17486	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1978085	0.92[ASN][1000 genomes]
rs2283041	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2299428	0.93[ASN][1000 genomes]
rs2395880	0.86[ASN][1000 genomes]
rs2395881	0.86[ASN][1000 genomes]
rs34084719	0.92[ASN][1000 genomes]
rs34523267	0.93[ASN][1000 genomes]
rs3779497	0.87[ASN][1000 genomes]
rs4515482	0.86[ASN][1000 genomes]
rs4727683	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4730248	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs4730250	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56949084	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6945784	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6947674	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6955488	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6957186	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6958969	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6964395	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6976759	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6979198	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6979368	0.90[ASN][1000 genomes]
rs763386	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7784906	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7785085	0.86[AMR][1000 genomes]
rs7797791	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7801317	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7807154	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8180747	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	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
2	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
3	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
4	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
5	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
6	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
7	nsv608074	chr7:107179131-107260856	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12056231	GPR22	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107154000-107193800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr7:107156400-107195000	Weak transcription	Colon Smooth Muscle	Colon
3	chr7:107162200-107203400	Weak transcription	Fetal Kidney	kidney
4	chr7:107166600-107194600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr7:107169600-107186400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr7:107170200-107203600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr7:107172800-107200200	Weak transcription	Psoas Muscle	Psoas
8	chr7:107176800-107187400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr7:107178600-107194200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr7:107178800-107194400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr7:107179400-107203200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr7:107182800-107186200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:107182800-107186600	Strong transcription	Stomach Smooth Muscle	stomach
14	chr7:107182800-107188400	Strong transcription	Duodenum Mucosa	Duodenum
15	chr7:107183000-107186200	ZNF genes & repeats	Fetal Stomach	stomach
16	chr7:107183000-107186400	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
17	chr7:107183000-107187400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr7:107183000-107188600	Strong transcription	Hela-S3	cervix
19	chr7:107183200-107188400	Strong transcription	Dnd41	blood
20	chr7:107183200-107198800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr7:107183600-107186600	ZNF genes & repeats	Fetal Intestine Large	intestine
22	chr7:107183600-107188000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr7:107183600-107188200	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr7:107183600-107188200	Strong transcription	HUVEC	blood vessel
25	chr7:107183600-107189000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:107183800-107186600	Strong transcription	NHEK	skin
27	chr7:107183800-107187000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr7:107183800-107188600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr7:107184000-107186400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr7:107184000-107187200	ZNF genes & repeats	Fetal Intestine Small	intestine
31	chr7:107184000-107187800	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr7:107184200-107186200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr7:107184200-107188400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr7:107184400-107186200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr7:107184400-107186600	ZNF genes & repeats	GM12878-XiMat	blood
36	chr7:107184400-107187800	Strong transcription	Colonic Mucosa	Colon
37	chr7:107184400-107188200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
38	chr7:107184400-107188200	Strong transcription	Placenta	Placenta
39	chr7:107184400-107188200	Strong transcription	NHDF-Ad	bronchial
40	chr7:107184400-107189000	Strong transcription	Fetal Thymus	thymus
41	chr7:107184600-107186200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
42	chr7:107184600-107187200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr7:107184600-107188000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr7:107184600-107188200	Strong transcription	Rectal Smooth Muscle	rectum
45	chr7:107184600-107195800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr7:107184800-107186200	ZNF genes & repeats	Lung	lung
47	chr7:107184800-107186600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
48	chr7:107184800-107186800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr7:107184800-107186800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr7:107184800-107186800	Strong transcription	HMEC	breast

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