Variant report

Variant	rs60515154
Chromosome Location	chr4:47914545-47914546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr4:47914534-47914572	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:47912116..47914767-chr4:47915076..47916747,3	MCF-7	breast:
2	chr4:47914296..47917191-chr4:48017364..48021197,5	MCF-7	breast:

Variant related genes	Relation type
NIPAL1	TF binding region
ENSG00000170448	Chromatin interaction
ENSG00000163293	Chromatin interaction
ENSG00000198515	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10025104	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10030927	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10938503	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12503789	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1371730	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1440227	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1507922	0.91[EUR][1000 genomes]
rs1583808	0.88[ASN][1000 genomes]
rs16860723	0.92[ASN][1000 genomes]
rs17654669	0.81[ASN][1000 genomes]
rs2033897	0.89[ASN][1000 genomes]
rs2033898	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2053404	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2289433	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2352145	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28464733	0.81[EUR][1000 genomes]
rs4529019	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4694867	0.89[ASN][1000 genomes]
rs4694872	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4695277	0.89[ASN][1000 genomes]
rs4695285	0.89[ASN][1000 genomes]
rs4695286	0.89[ASN][1000 genomes]
rs4695290	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4695292	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4695300	0.92[ASN][1000 genomes]
rs4695303	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4695306	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4695307	0.93[ASN][1000 genomes]
rs4695308	0.93[ASN][1000 genomes]
rs57010305	0.92[ASN][1000 genomes]
rs58511183	0.92[ASN][1000 genomes]
rs60427744	0.92[ASN][1000 genomes]
rs6414687	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447586	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6447592	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447593	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6811385	0.92[ASN][1000 genomes]
rs6816082	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6818556	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6822668	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6827508	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6844286	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73238638	0.87[ASN][1000 genomes]
rs73238639	0.89[ASN][1000 genomes]
rs73244433	0.89[ASN][1000 genomes]
rs73244436	0.91[ASN][1000 genomes]
rs73244437	0.91[ASN][1000 genomes]
rs73244438	0.92[ASN][1000 genomes]
rs73244439	0.92[ASN][1000 genomes]
rs73244442	0.89[ASN][1000 genomes]
rs7663935	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7687363	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7690562	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs920462	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9291317	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9683791	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs60515154	CNGA1	cis	Muscle Skeletal	GTEx
rs60515154	CNGA1	cis	Heart Left Ventricle	GTEx
rs60515154	CNGA1	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47876000-47915200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:47876200-47915200	Weak transcription	Right Ventricle	heart
3	chr4:47876400-47915200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr4:47876800-47915800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:47882200-47915200	Weak transcription	Stomach Mucosa	stomach
6	chr4:47894600-47915200	Weak transcription	Aorta	Aorta
7	chr4:47894600-47915200	Weak transcription	Gastric	stomach
8	chr4:47898200-47915200	Weak transcription	Small Intestine	intestine
9	chr4:47898400-47915000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:47898400-47915200	Weak transcription	Colonic Mucosa	Colon
11	chr4:47898600-47915200	Weak transcription	Fetal Brain Male	brain
12	chr4:47899600-47915600	Weak transcription	Lung	lung
13	chr4:47899800-47915000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:47899800-47915200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:47899800-47915200	Weak transcription	Brain Substantia Nigra	brain
16	chr4:47900000-47915200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:47900200-47915200	Weak transcription	HSMMtube	muscle
18	chr4:47900600-47915200	Weak transcription	Thymus	Thymus
19	chr4:47901000-47915200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr4:47901000-47915200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr4:47901000-47915200	Weak transcription	Stomach Smooth Muscle	stomach
22	chr4:47901200-47915000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr4:47901200-47915200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr4:47901400-47915200	Weak transcription	Colon Smooth Muscle	Colon
25	chr4:47902000-47915200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr4:47902600-47915200	Weak transcription	Pancreas	Pancrea
27	chr4:47905200-47915200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:47906600-47915000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:47906600-47915200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr4:47906600-47915200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr4:47906600-47915200	Weak transcription	Spleen	Spleen
32	chr4:47906600-47915400	Weak transcription	Esophagus	oesophagus
33	chr4:47906800-47915200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr4:47906800-47915600	Weak transcription	Left Ventricle	heart
35	chr4:47907000-47915200	Weak transcription	Brain Hippocampus Middle	brain
36	chr4:47907800-47915200	Weak transcription	Brain Germinal Matrix	brain
37	chr4:47907800-47915200	Weak transcription	Psoas Muscle	Psoas
38	chr4:47908200-47915200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr4:47908200-47915200	Weak transcription	Brain Angular Gyrus	brain
40	chr4:47908600-47915200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr4:47909400-47915200	Weak transcription	NHDF-Ad	bronchial
42	chr4:47909600-47915000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:47909600-47915200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr4:47910200-47915200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr4:47910200-47915200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:47910200-47915200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr4:47910200-47915200	Weak transcription	HSMM	muscle
48	chr4:47910400-47915200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr4:47910400-47915200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr4:47910600-47915200	Weak transcription	Primary B cells from peripheral blood	blood

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