Variant report

Variant	rs4266424
Chromosome Location	chr5:95996883-95996884
allele	A/C
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	chr5:95996816-95996975	Hela-S3	cervix:	n/a	n/a
2	CTCF	chr5:95996740-95996890	AG09319	gingival:	n/a	n/a
3	CTCF	chr5:95996820-95996970	GM12871	blood:	n/a	n/a
4	RELA	chr5:95996828-95998689	GM19099	blood:	n/a	n/a
5	REST	chr5:95996871-95998155	A549	lung:	n/a	chr5:95997353-95997360 chr5:95998007-95998017
6	POLR2A	chr5:95996266-96000322	Hela-S3	cervix:	n/a	n/a
7	ZNF384	chr5:95996593-95997882	GM12878	blood:	n/a	n/a
8	SIX5	chr5:95996865-95997815	A549	lung:	n/a	n/a
9	MAX	chr5:95996810-95997980	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:95996562-95999133	U87	brain:	n/a	n/a
11	TCF7L2	chr5:95996819-95999548	Hela-S3	cervix:	n/a	chr5:95999358-95999372 chr5:95999233-95999242 chr5:95999230-95999244 chr5:95999229-95999245 chr5:95999229-95999245

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:65274341..65275303-chr5:95996277..95997185,2	Hela-S3	cervix:
2	chr5:95994913..95997156-chr5:96000541..96002076,2	MCF-7	breast:

Variant related genes	Relation type
CAST	TF binding region

Extended variants
information (count: 6 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs149319	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6556938	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024964	chr5:95742124-96065492	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv537811	chr5:95742124-96065492	Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1015173	chr5:95987366-96153392	Genic enhancers Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4266424	CAST	cis	Nerve Tibial	GTEx
rs4266424	CTC-506B8.1	cis	Whole Blood	GTEx
rs4266424	CAST	cis	lung	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95992200-95997600	Weak transcription	Gastric	stomach
2	chr5:95992400-95997200	Weak transcription	Esophagus	oesophagus
3	chr5:95994200-95997000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:95994200-95997000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:95994600-95997200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:95995200-95997200	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr5:95995800-95997000	Enhancers	Stomach Mucosa	stomach
8	chr5:95996000-95997000	Enhancers	Placenta Amnion	Placenta Amnion
9	chr5:95996200-95997000	Enhancers	NH-A	brain
10	chr5:95996200-95997200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr5:95996400-95997000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr5:95996400-95997000	Enhancers	Fetal Heart	heart
13	chr5:95996400-95997000	Flanking Active TSS	GM12878-XiMat	blood
14	chr5:95996400-95997200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
15	chr5:95996400-95997400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:95996400-95997600	Flanking Active TSS	Hela-S3	cervix
17	chr5:95996400-95997600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr5:95996400-95998000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr5:95996600-95997000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:95996600-95997000	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr5:95996600-95997000	Flanking Active TSS	Primary T cells from cord blood	blood
22	chr5:95996600-95997000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:95996600-95997000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr5:95996600-95997000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
25	chr5:95996600-95997000	Flanking Active TSS	Placenta	Placenta
26	chr5:95996600-95997000	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr5:95996600-95997000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr5:95996600-95997000	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr5:95996600-95997000	Flanking Active TSS	Dnd41	blood
30	chr5:95996600-95997000	Flanking Active TSS	HMEC	breast
31	chr5:95996600-95997200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr5:95996600-95997200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
33	chr5:95996600-95997200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:95996600-95997200	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr5:95996600-95997200	Flanking Active TSS	Fetal Muscle Leg	muscle
36	chr5:95996600-95997200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
37	chr5:95996600-95997400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
38	chr5:95996600-95997400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
39	chr5:95996600-95997400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr5:95996600-95997400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr5:95996600-95997400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
42	chr5:95996600-95997600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
43	chr5:95996600-95997600	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr5:95996600-95997600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr5:95996600-95997600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr5:95996600-95997600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr5:95996600-95997600	Flanking Active TSS	NHEK	skin
48	chr5:95996600-95998000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr5:95996600-95998400	Active TSS	Fetal Brain Female	brain
50	chr5:95996600-95999000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links