Variant report

Variant	rs28636596
Chromosome Location	chr4:47915328-47915329
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TAL1	chr4:47915207-47916041	K562	blood:	n/a	n/a
2	POLR2A	chr4:47915315-47917247	GM12891	blood:	n/a	n/a
3	TEAD4	chr4:47915286-47915732	HepG2	liver:	n/a	n/a
4	SETDB1	chr4:47915113-47917096	K562	blood:	n/a	chr4:47916758-47916767 chr4:47916788-47916812
5	KAP1	chr4:47915226-47917155	HEK293	kidney:	n/a	n/a
6	CBX3	chr4:47915314-47915625	K562	blood:	n/a	n/a
7	MXI1	chr4:47915166-47917322	IMR90	lung:	n/a	n/a
8	TRIM28	chr4:47915242-47915936	K562	blood:	n/a	n/a
9	POLR2A	chr4:47915130-47917127	K562	blood:	n/a	n/a
10	TRIM28	chr4:47915264-47915664	K562	blood:	n/a	n/a
11	KAP1	chr4:47915316-47915685	K562	blood:	n/a	n/a
12	SETDB1	chr4:47915285-47915616	U2OS	brain:	n/a	n/a
13	POLR2A	chr4:47915130-47917260	H1-hESC	embryonic stem cell:	n/a	n/a
14	TEAD4	chr4:47915265-47915811	K562	blood:	n/a	n/a
15	CHD2	chr4:47915317-47915471	HepG2	liver:	n/a	n/a
16	TEAD4	chr4:47915298-47915675	K562	blood:	n/a	n/a
17	ZNF143	chr4:47915294-47915840	K562	blood:	n/a	n/a
18	CBX3	chr4:47915160-47915962	K562	blood:	n/a	n/a
19	BHLHE40	chr4:47915236-47915674	K562	blood:	n/a	n/a
20	RCOR1	chr4:47915326-47917062	K562	blood:	n/a	n/a
21	POLR2A	chr4:47915179-47917251	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:47914296..47917191-chr4:48017364..48021197,5	MCF-7	breast:
2	chr4:47915045..47916605-chr4:48017433..48018940,2	MCF-7	breast:

No data

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

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10008818	0.84[EUR][1000 genomes]
rs10028155	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10049713	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1012844	0.83[EUR][1000 genomes]
rs1062858	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10938499	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10938500	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10938504	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10938505	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10938506	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12186152	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12504018	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12506632	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12507439	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12510002	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12641871	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12651301	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1371729	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1371731	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1440228	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17463666	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17573709	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1822030	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866689	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1984713	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2033893	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2289435	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2352470	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28395298	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28412313	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28460483	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28573115	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28583602	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4435717	0.84[EUR][1000 genomes]
rs4565052	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56001837	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6447587	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6447589	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6811177	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6823184	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6823698	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6833758	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6858440	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8180146	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs978094	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9994561	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9995122	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9997555	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs28636596	CNGA1	cis	Adipose Subcutaneous	GTEx
rs28636596	CNGA1	cis	Heart Left Ventricle	GTEx
rs28636596	NFXL1	cis	Whole Blood	GTEx
rs28636596	CNGA1	cis	Muscle Skeletal	GTEx
rs28636596	CORIN	cis	Whole Blood	GTEx
rs28636596	RP11-121C2.2	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47876800-47915800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr4:47899600-47915600	Weak transcription	Lung	lung
3	chr4:47906600-47915400	Weak transcription	Esophagus	oesophagus
4	chr4:47906800-47915600	Weak transcription	Left Ventricle	heart
5	chr4:47911200-47915600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr4:47913400-47917200	Active TSS	Muscle Satellite Cultured Cells	--
7	chr4:47914200-47917400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr4:47914400-47917000	Active TSS	GM12878-XiMat	blood
9	chr4:47914400-47917400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:47914400-47917600	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr4:47914400-47917600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr4:47914600-47915600	Enhancers	Primary T cells fromperipheralblood	blood
13	chr4:47915000-47915400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
14	chr4:47915000-47915400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:47915000-47915400	Enhancers	Placenta Amnion	Placenta Amnion
16	chr4:47915000-47915400	Flanking Active TSS	Hela-S3	cervix
17	chr4:47915000-47915400	Flanking Active TSS	HepG2	liver
18	chr4:47915000-47915600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr4:47915000-47915600	Flanking Active TSS	NHEK	skin
20	chr4:47915000-47916000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr4:47915000-47916000	Flanking Active TSS	Dnd41	blood
22	chr4:47915000-47916000	Flanking Active TSS	HUVEC	blood vessel
23	chr4:47915000-47916000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr4:47915000-47916800	Active TSS	NHLF	lung
25	chr4:47915000-47917200	Active TSS	HMEC	breast
26	chr4:47915000-47917400	Active TSS	H1 Cell Line	embryonic stem cell
27	chr4:47915000-47917400	Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr4:47915000-47917400	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr4:47915000-47917600	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr4:47915200-47915400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:47915200-47915400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr4:47915200-47915400	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:47915200-47915400	Enhancers	Primary T cells from cord blood	blood
34	chr4:47915200-47915400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr4:47915200-47915400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:47915200-47915400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr4:47915200-47915400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr4:47915200-47915400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr4:47915200-47915400	Enhancers	Adipose Nuclei	Adipose
40	chr4:47915200-47915400	Enhancers	Brain Angular Gyrus	brain
41	chr4:47915200-47915400	Flanking Active TSS	Colonic Mucosa	Colon
42	chr4:47915200-47915400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr4:47915200-47915400	Enhancers	Fetal Intestine Small	intestine
44	chr4:47915200-47915400	Flanking Active TSS	Fetal Kidney	kidney
45	chr4:47915200-47915400	Enhancers	Fetal Muscle Leg	muscle
46	chr4:47915200-47915400	Enhancers	Fetal Stomach	stomach
47	chr4:47915200-47915400	Enhancers	Fetal Thymus	thymus
48	chr4:47915200-47915400	Enhancers	Gastric	stomach
49	chr4:47915200-47915400	Enhancers	Right Atrium	heart
50	chr4:47915200-47915400	Enhancers	Skeletal Muscle Female	skeletal muscle

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