Variant report

Variant	rs11722463
Chromosome Location	chr4:48038716-48038717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11733284	0.98[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11736427	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13120847	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13125949	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13140968	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13142905	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13146880	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs321622	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs321628	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs321630	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs321631	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4694879	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4695328	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6811245	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6832503	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6835057	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs98270	0.86[EUR][1000 genomes];0.97[ASN][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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv967990	chr4:48037803-48041600	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11722463	CNGA1	cis	Esophagus Muscularis	GTEx
rs11722463	CNGA1	cis	Adipose Subcutaneous	GTEx
rs11722463	CNGA1	cis	Heart Left Ventricle	GTEx
rs11722463	CNGA1	cis	Muscle Skeletal	GTEx
rs11722463	CNGA1	cis	Thyroid	GTEx
rs11722463	NIPAL1	cis	lung	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48043600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
3	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
4	chr4:48024600-48043600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:48026800-48045400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:48028200-48040800	Weak transcription	Gastric	stomach
7	chr4:48028200-48042600	Weak transcription	Placenta	Placenta
8	chr4:48031600-48041800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr4:48032800-48045000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr4:48033000-48045000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr4:48034200-48049600	Weak transcription	Pancreas	Pancrea
12	chr4:48034400-48039400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:48034800-48039200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:48034800-48041600	Strong transcription	HMEC	breast
15	chr4:48035000-48039000	Weak transcription	Hela-S3	cervix
16	chr4:48035800-48040200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr4:48036000-48040400	Enhancers	Primary B cells from peripheral blood	blood
18	chr4:48036200-48040000	Weak transcription	HepG2	liver
19	chr4:48036200-48041000	Enhancers	Primary B cells from cord blood	blood
20	chr4:48036400-48046400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr4:48036600-48040400	Weak transcription	Fetal Intestine Small	intestine
22	chr4:48037000-48039000	Strong transcription	Fetal Intestine Large	intestine
23	chr4:48037000-48039800	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr4:48037800-48039000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr4:48037800-48039600	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr4:48038000-48039000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr4:48038000-48039000	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr4:48038000-48042800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:48038000-48044600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr4:48038000-48044800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:48038000-48047800	Weak transcription	NHEK	skin
32	chr4:48038200-48039000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr4:48038200-48040200	Weak transcription	Liver	Liver
34	chr4:48038200-48044400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr4:48038200-48045200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:48038400-48038800	Enhancers	GM12878-XiMat	blood
37	chr4:48038400-48044600	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr4:48038600-48038800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr4:48038600-48039400	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr4:48038600-48043600	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr4:48038600-48045200	Weak transcription	Fetal Heart	heart
42	chr4:48038600-48053000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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