Variant report

Variant	rs6573857
Chromosome Location	chr14:69263074-69263075
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:396)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:396 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr14:69262697-69263180	K562	blood:	n/a	n/a
2	ELF1	chr14:69262560-69263411	HepG2	liver:	n/a	n/a
3	EP300	chr14:69262333-69264410	K562	blood:	n/a	n/a
4	NFIC	chr14:69258747-69263739	GM12878	blood:	n/a	n/a
5	POLR2A	chr14:69250963-69263207	U87	brain:	n/a	n/a
6	TBP	chr14:69262270-69263427	GM12878	blood:	n/a	n/a
7	CTCF	chr14:69263000-69263150	HPF	lung:	n/a	n/a
8	ZNF143	chr14:69262580-69263435	H1-hESC	embryonic stem cell:	n/a	n/a
9	CREB1	chr14:69262133-69263492	H1-hESC	embryonic stem cell:	n/a	n/a
10	RAD21	chr14:69262215-69263441	H1-hESC	embryonic stem cell:	n/a	n/a
11	GATA1	chr14:69262430-69264491	PBDE	blood:	n/a	chr14:69263876-69263883 chr14:69263876-69263883 chr14:69263876-69263883 chr14:69263767-69263776 chr14:69263869-69263890
12	CTCF	chr14:69262153-69263392	GM12878	blood:	n/a	n/a
13	RELA	chr14:69258539-69263496	GM12891	blood:	n/a	n/a
14	BHLHE40	chr14:69259293-69263433	GM12878	blood:	n/a	n/a
15	MAX	chr14:69259345-69263353	K562	blood:	n/a	n/a
16	BCL11A	chr14:69263001-69263363	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr14:69262126-69263147	MCF-7	breast:	n/a	n/a
18	PML	chr14:69258860-69263235	MCF-7	breast:	n/a	n/a
19	TCF3	chr14:69262157-69263439	GM12878	blood:	n/a	n/a
20	CTCF	chr14:69262646-69263149	GM12891	blood:	n/a	n/a
21	ELF1	chr14:69262563-69263256	K562	blood:	n/a	n/a
22	CHD2	chr14:69262155-69263138	K562	blood:	n/a	n/a
23	NFIC	chr14:69262979-69263481	HepG2	liver:	n/a	n/a
24	POLR2A	chr14:69254988-69263278	GM12892	blood:	n/a	n/a
25	JUND	chr14:69262988-69263137	H1-hESC	embryonic stem cell:	n/a	n/a
26	NFYB	chr14:69262790-69263234	GM12878	blood:	n/a	n/a
27	BCL11A	chr14:69262916-69263358	GM12878	blood:	n/a	n/a
28	POU2F2	chr14:69262258-69263134	GM12878	blood:	n/a	n/a
29	POLR2A	chr14:69255614-69263201	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr14:69254928-69263445	GM12892	blood:	n/a	n/a
31	EP300	chr14:69258805-69263522	ECC-1	luminal epithelium:	n/a	chr14:69260104-69260120 chr14:69260038-69260052 chr14:69261261-69261270 chr14:69260641-69260657 chr14:69259995-69260009 chr14:69260648-69260657
32	POLR2A	chr14:69257221-69263637	MCF10A-Er-Src	breast:	n/a	n/a
33	TEAD4	chr14:69262227-69263522	ECC-1	luminal epithelium:	n/a	n/a
34	FOSL2	chr14:69262571-69263534	A549	lung:	n/a	n/a
35	MTA3	chr14:69254975-69264454	GM12878	blood:	n/a	n/a
36	EP300	chr14:69261098-69263133	SK-N-SH	brain:	n/a	chr14:69261261-69261270
37	TCF12	chr14:69262966-69263402	GM12878	blood:	n/a	n/a
38	MEF2A	chr14:69262186-69263461	GM12878	blood:	n/a	n/a
39	POLR2A	chr14:69257126-69263442	GM12891	blood:	n/a	n/a
40	CREB1	chr14:69259245-69263453	GM12878	blood:	n/a	chr14:69260175-69260188
41	TAF1	chr14:69262185-69263205	Hela-S3	cervix:	n/a	n/a
42	E2F6	chr14:69261926-69263253	K562	blood:	n/a	chr14:69262660-69262671
43	POLR2A	chr14:69259992-69263223	GM12891	blood:	n/a	n/a
44	YY1	chr14:69262126-69263413	GM12878	blood:	n/a	n/a
45	CBX3	chr14:69262986-69263505	K562	blood:	n/a	n/a
46	POLR2A	chr14:69256736-69263833	Raji	blood:	n/a	n/a
47	E2F6	chr14:69262034-69263540	A549	lung:	n/a	chr14:69262660-69262671
48	POLR2A	chr14:69255146-69263257	GM18526	blood:	n/a	n/a
49	TCF3	chr14:69262966-69263373	GM12878	blood:	n/a	n/a
50	SIN3A	chr14:69262127-69263226	GM12878	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:69090615..69103406-chr14:69249821..69264188,29	MCF-7	breast:
2	chr14:68140439..68142137-chr14:69262660..69264249,2	MCF-7	breast:
3	chr14:69261403..69263120-chr2:70313914..70316078,2	MCF-7	breast:
4	chr14:69262582..69264227-chr20:45984862..45986463,2	MCF-7	breast:
5	chr14:68930492..68947840-chr14:69251918..69264148,62	MCF-7	breast:
6	chr14:68852547..68854208-chr14:69260882..69263512,3	MCF-7	breast:
7	chr14:69091753..69104091-chr14:69256141..69263760,20	MCF-7	breast:
8	chr12:80328974..80330991-chr14:69261768..69263404,2	MCF-7	breast:
9	chr14:69260918..69263431-chr14:69412114..69414632,2	MCF-7	breast:
10	chr14:69258720..69263996-chr17:57918463..57922385,5	MCF-7	breast:
11	chr14:68853558..68855258-chr14:69259341..69263299,3	MCF-7	breast:
12	chr14:69259571..69263343-chr17:57914028..57917030,5	MCF-7	breast:
13	chr14:69201544..69205045-chr14:69260784..69263529,4	K562	blood:

No data

Variant related genes	Relation type
ZFP36L1	TF binding region
ENSG00000062716	Chromatin interaction
ENSG00000182185	Chromatin interaction
ENSG00000169564	Chromatin interaction
ENSG00000072110	Chromatin interaction
ENSG00000058272	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000179818	Chromatin interaction
ENSG00000207089	Chromatin interaction
ENSG00000259038	Chromatin interaction
ENSG00000100568	Chromatin interaction
ENSG00000199004	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10142466	0.94[ASN][1000 genomes]
rs11158762	0.81[JPT][hapmap]
rs11626883	0.94[ASN][1000 genomes]
rs12889006	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs1465788	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1595260	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1595261	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17106304	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17835641	0.94[ASN][1000 genomes]
rs17835647	0.94[ASN][1000 genomes]
rs1836984	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs194748	0.91[ASN][1000 genomes]
rs194749	0.96[ASN][1000 genomes]
rs194751	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs194778	0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2236262	1.00[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs2236263	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34489253	0.97[ASN][1000 genomes]
rs367677	0.88[ASN][1000 genomes]
rs3742887	0.89[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3825568	1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs4899258	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4899259	0.91[ASN][1000 genomes]
rs4902651	0.94[ASN][1000 genomes]
rs7146217	0.88[JPT][hapmap]
rs7149271	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7156516	0.91[ASN][1000 genomes]
rs8011558	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8022092	0.97[ASN][1000 genomes]
rs927292	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035267	chr14:69230254-69348126	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv542123	chr14:69230254-69348126	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	nsv902070	chr14:69244214-69308182	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6573857	ZFP36L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69255400-69263200	Active TSS	Pancreatic Islets	Pancreatic Islet
2	chr14:69256400-69263200	Active TSS	Primary T cells from cord blood	blood
3	chr14:69256800-69263200	Active TSS	Small Intestine	intestine
4	chr14:69257200-69263200	Active TSS	Aorta	Aorta
5	chr14:69257200-69263400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr14:69257200-69263600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
7	chr14:69257200-69263800	Active TSS	H9 Cell Line	embryonic stem cell
8	chr14:69257400-69263200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr14:69257400-69263200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr14:69257400-69263200	Active TSS	Ovary	ovary
11	chr14:69257400-69263200	Active TSS	Spleen	Spleen
12	chr14:69257400-69263400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr14:69257600-69263200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr14:69257600-69263200	Active TSS	Fetal Kidney	kidney
15	chr14:69257600-69263200	Active TSS	Gastric	stomach
16	chr14:69257600-69263400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr14:69257800-69263400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr14:69258000-69263200	Active TSS	Psoas Muscle	Psoas
19	chr14:69258000-69263400	Active TSS	H1 Cell Line	embryonic stem cell
20	chr14:69258200-69263200	Active TSS	Right Ventricle	heart
21	chr14:69258200-69263400	Active TSS	HUES64 Cell Line	embryonic stem cell
22	chr14:69258400-69263200	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr14:69258400-69263200	Active TSS	Left Ventricle	heart
24	chr14:69258400-69263400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr14:69258600-69263200	Active TSS	Placenta Amnion	Placenta Amnion
26	chr14:69258600-69263400	Active TSS	Colonic Mucosa	Colon
27	chr14:69258800-69263400	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr14:69259600-69263200	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr14:69259800-69263200	Active TSS	Colon Smooth Muscle	Colon
30	chr14:69260600-69263200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr14:69261200-69263200	Bivalent/Poised TSS	Fetal Brain Female	brain
32	chr14:69261400-69263200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr14:69261600-69263200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr14:69261600-69263400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
35	chr14:69261800-69263200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr14:69261800-69263200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr14:69262000-69263200	Active TSS	Brain Angular Gyrus	brain
38	chr14:69262200-69263200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
39	chr14:69262400-69263200	Transcr. at gene 5' and 3'	Right Atrium	heart
40	chr14:69262400-69263400	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr14:69262600-69263200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr14:69262600-69263200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr14:69262600-69263600	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr14:69262600-69263800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr14:69262600-69264200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr14:69262800-69263200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr14:69262800-69263200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
48	chr14:69262800-69263200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr14:69262800-69263200	Flanking Active TSS	HMEC	breast
50	chr14:69262800-69263200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links