Variant report

Variant	rs2434217
Chromosome Location	chr5:154214852-154214853
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:126)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	UBTF	chr5:154214132-154214999	K562	blood:	n/a	n/a
2	CEBPB	chr5:154214649-154215176	Hela-S3	cervix:	n/a	chr5:154214806-154214817
3	GTF2B	chr5:154214416-154214993	K562	blood:	n/a	n/a
4	CREB1	chr5:154214168-154215226	K562	blood:	n/a	n/a
5	GATA2	chr5:154214344-154215126	K562	blood:	n/a	n/a
6	SIN3AK20	chr5:154214345-154214852	K562	blood:	n/a	n/a
7	SP1	chr5:154214365-154215214	K562	blood:	n/a	chr5:154214497-154214511 chr5:154214719-154214733
8	GATA3	chr5:154214481-154215154	MCF-7	breast:	n/a	n/a
9	GATA1	chr5:154213995-154215358	K562	blood:	n/a	n/a
10	POLR2A	chr5:154214287-154215208	K562	blood:	n/a	n/a
11	STAT3	chr5:154214804-154215193	MCF10A-Er-Src	breast:	n/a	n/a
12	ATF1	chr5:154214381-154215115	K562	blood:	n/a	n/a
13	GATA1	chr5:154214431-154214960	PBDEFetal	blood:	n/a	n/a
14	ZNF143	chr5:154214313-154215121	K562	blood:	n/a	n/a
15	POLR2A	chr5:154214756-154215121	MCF10A-Er-Src	breast:	n/a	n/a
16	ZMIZ1	chr5:154214239-154215068	K562	blood:	n/a	n/a
17	POLR2A	chr5:154214415-154215224	U87	brain:	n/a	n/a
18	EGR1	chr5:154214488-154214865	K562	blood:	n/a	n/a
19	RCOR1	chr5:154214297-154215217	K562	blood:	n/a	n/a
20	NFYA	chr5:154214418-154215083	K562	blood:	n/a	n/a
21	REST	chr5:154214225-154214927	K562	blood:	n/a	chr5:154214330-154214339 chr5:154214333-154214341
22	TAL1	chr5:154214213-154215177	K562	blood:	n/a	chr5:154214660-154214678
23	CEBPB	chr5:154214624-154215104	HepG2	liver:	n/a	chr5:154214806-154214817
24	TBL1XR1	chr5:154214260-154215099	K562	blood:	n/a	n/a
25	POLR2A	chr5:154214198-154214992	PBDE	blood:	n/a	n/a
26	ARID3A	chr5:154214487-154215117	K562	blood:	n/a	n/a
27	NFIC	chr5:154214800-154215245	ECC-1	luminal epithelium:	n/a	n/a
28	GATA3	chr5:154214402-154215253	SK-N-SH	brain:	n/a	n/a
29	ZNF384	chr5:154213817-154215222	K562	blood:	n/a	n/a
30	POLR2A	chr5:154214504-154215132	SK-N-SH	brain:	n/a	n/a
31	REST	chr5:154214160-154215154	K562	blood:	n/a	chr5:154214330-154214339 chr5:154214333-154214341
32	IRF1	chr5:154214370-154215065	K562	blood:	n/a	n/a
33	ELF1	chr5:154214358-154214857	K562	blood:	n/a	n/a
34	ETS1	chr5:154214380-154214872	K562	blood:	n/a	n/a
35	MAFK	chr5:154214432-154215114	K562	blood:	n/a	n/a
36	NFIC	chr5:154214592-154215259	SK-N-SH	brain:	n/a	n/a
37	CUX1	chr5:154214226-154215153	K562	blood:	n/a	n/a
38	CEBPB	chr5:154214655-154215226	MCF-7	breast:	n/a	chr5:154214806-154214817
39	RCOR1	chr5:154214135-154215196	K562	blood:	n/a	n/a
40	NFIC	chr5:154214736-154215261	ECC-1	luminal epithelium:	n/a	n/a
41	IRF1	chr5:154214083-154215121	K562	blood:	n/a	n/a
42	POLR2A	chr5:154214252-154214858	K562	blood:	n/a	n/a
43	EP300	chr5:154214143-154215162	K562	blood:	n/a	n/a
44	CEBPB	chr5:154214392-154215158	K562	blood:	n/a	chr5:154214806-154214817
45	NR2F2	chr5:154214339-154215169	K562	blood:	n/a	n/a
46	GATA3	chr5:154214772-154215209	T-47D	breast:	n/a	n/a
47	POLR2A	chr5:154214229-154215205	K562	blood:	n/a	n/a
48	HMGN3	chr5:154214266-154215111	K562	blood:	n/a	n/a
49	MAX	chr5:154214391-154215138	K562	blood:	n/a	n/a
50	FOS	chr5:154214714-154215219	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:154209594..154211615-chr5:154213176..154215007,2	K562	blood:
2	chr5:154207634..154212086-chr5:154212438..154216728,14	MCF-7	breast:
3	chr5:154205913..154219158-chr5:154234172..154242635,38	MCF-7	breast:
4	chr5:154212721..154214972-chr5:154234901..154239444,4	K562	blood:
5	chr5:154133720..154135863-chr5:154214585..154216471,2	K562	blood:
6	chr5:154209529..154211376-chr5:154214452..154217277,2	K562	blood:
7	chr5:154214026..154216712-chr5:154234654..154237422,2	K562	blood:

No data

Variant related genes	Relation type
FAXDC2	TF binding region
ENSG00000155508	Chromatin interaction
ENSG00000155506	Chromatin interaction
ENSG00000263361	Chromatin interaction
ENSG00000170271	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs13153640	0.84[TSI][hapmap]
rs13156153	0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13156669	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13164115	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs13182236	0.85[TSI][hapmap]
rs1403559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2434218	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2544891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6882998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs816735	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2434217	CNOT8	cis	Skin Sun Exposed Lower leg	GTEx
rs2434217	CNOT8	cis	Nerve Tibial	GTEx
rs2434217	CNOT8	cis	lung	GTEx
rs2434217	CNOT8	cis	Adipose Subcutaneous	GTEx
rs2434217	CNOT8	cis	Thyroid	GTEx
rs2434217	CNOT8	cis	Artery Tibial	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154196000-154229200	Weak transcription	Psoas Muscle	Psoas
2	chr5:154201000-154228000	Weak transcription	Fetal Brain Male	brain
3	chr5:154203400-154229000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:154210200-154229000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:154210600-154215000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
6	chr5:154210800-154229000	Weak transcription	Fetal Kidney	kidney
7	chr5:154210800-154229800	Weak transcription	Fetal Thymus	thymus
8	chr5:154211000-154216600	Weak transcription	Fetal Lung	lung
9	chr5:154211200-154217200	Weak transcription	Spleen	Spleen
10	chr5:154211400-154217400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:154211400-154221600	Weak transcription	Thymus	Thymus
12	chr5:154211400-154228800	Weak transcription	Fetal Brain Female	brain
13	chr5:154211400-154229400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:154211400-154229400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:154211400-154229800	Weak transcription	Pancreas	Pancrea
16	chr5:154211400-154235800	Weak transcription	Dnd41	blood
17	chr5:154211600-154220400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr5:154211600-154220600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr5:154211800-154222600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr5:154211800-154229000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:154211800-154229200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:154212200-154215800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr5:154212400-154229200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr5:154212600-154229400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr5:154212800-154216400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:154213800-154215200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr5:154213800-154215200	Flanking Active TSS	K562	blood
28	chr5:154213800-154215800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:154213800-154215800	Enhancers	HMEC	breast
30	chr5:154214000-154215000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr5:154214000-154215200	Genic enhancers	Muscle Satellite Cultured Cells	--
32	chr5:154214000-154215200	Active TSS	Colon Smooth Muscle	Colon
33	chr5:154214000-154215200	Enhancers	Fetal Heart	heart
34	chr5:154214000-154215200	Genic enhancers	A549	lung
35	chr5:154214200-154215000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr5:154214200-154215000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:154214200-154215000	Enhancers	Placenta	Placenta
38	chr5:154214200-154215000	Enhancers	Stomach Mucosa	stomach
39	chr5:154214200-154215200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:154214200-154215200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr5:154214200-154215200	Enhancers	Duodenum Mucosa	Duodenum
42	chr5:154214200-154215200	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr5:154214200-154215200	Active TSS	Rectal Smooth Muscle	rectum
44	chr5:154214200-154215200	Enhancers	NH-A	brain
45	chr5:154214200-154215800	Enhancers	Ovary	ovary
46	chr5:154214200-154215800	Enhancers	Osteobl	bone
47	chr5:154214200-154216000	Enhancers	HSMMtube	muscle
48	chr5:154214400-154215000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr5:154214400-154215000	Enhancers	Skeletal Muscle Male	skeletal muscle
50	chr5:154214400-154215000	Flanking Active TSS	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links