Variant report

Variant	rs4902647
Chromosome Location	chr14:69254191-69254192
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:49)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:49 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:69095355..69099854-chr14:69250960..69255583,6	MCF-7	breast:
2	chr14:69090615..69103406-chr14:69249821..69264188,29	MCF-7	breast:
3	chr14:69177394..69179391-chr14:69252798..69254946,2	K562	blood:
4	chr14:69204312..69206697-chr14:69251799..69254255,2	K562	blood:
5	chr14:69252105..69254331-chr7:155601869..155604492,2	MCF-7	breast:
6	chr14:69128588..69133050-chr14:69253079..69257196,5	MCF-7	breast:
7	chr14:68407933..68410630-chr14:69252286..69254725,3	MCF-7	breast:
8	chr1:149222906..149224972-chr14:69253180..69255841,2	MCF-7	breast:
9	chr14:68351021..68355555-chr14:69252888..69257229,4	MCF-7	breast:
10	chr14:68641461..68644387-chr14:69250543..69254390,3	MCF-7	breast:
11	chr14:68714423..68716152-chr14:69252930..69254680,2	K562	blood:
12	chr14:69214304..69216670-chr14:69253517..69255895,2	K562	blood:
13	chr14:68930492..68947840-chr14:69251918..69264148,62	MCF-7	breast:
14	chr14:68704238..68708340-chr14:69251416..69255393,5	MCF-7	breast:
15	chr14:68958868..68960995-chr14:69252275..69254808,2	MCF-7	breast:
16	chr14:69175919..69179452-chr14:69252048..69254432,3	MCF-7	breast:
17	chr14:69010091..69012827-chr14:69253448..69255252,2	MCF-7	breast:
18	chr14:68876240..68877948-chr14:69253264..69255606,2	MCF-7	breast:
19	chr14:69054452..69058686-chr14:69249853..69254831,4	MCF-7	breast:
20	chr14:68605789..68607754-chr14:69253022..69255684,2	MCF-7	breast:
21	chr14:68658549..68661860-chr14:69250890..69254751,3	MCF-7	breast:
22	chr14:69254185..69254933-chr19:13264507..13265445,2	Hela-S3	cervix:
23	chr14:68881675..68884365-chr14:69252579..69254360,2	MCF-7	breast:
24	chr14:68299804..68301953-chr14:69252103..69254341,2	MCF-7	breast:
25	chr14:68951909..68954221-chr14:69252070..69254907,3	MCF-7	breast:
26	chr14:69253583..69254279-chr17:80186633..80187256,2	HCT-116	colon:
27	chr14:69043850..69046166-chr14:69253123..69255175,2	MCF-7	breast:
28	chr14:68740444..68743175-chr14:69252311..69254670,3	MCF-7	breast:
29	chr14:68827778..68831796-chr14:69251511..69256304,4	MCF-7	breast:
30	chr14:68659031..68663058-chr14:69251667..69256012,5	MCF-7	breast:
31	chr14:68850472..68852853-chr14:69251979..69254595,2	MCF-7	breast:
32	chr14:68744987..68750260-chr14:69250111..69256950,7	MCF-7	breast:
33	chr14:68697979..68700527-chr14:69251377..69254277,2	MCF-7	breast:
34	chr14:68405495..68411980-chr14:69250946..69254866,9	MCF-7	breast:
35	chr14:69197485..69199211-chr14:69252753..69254670,2	MCF-7	breast:
36	chr14:68630093..68632260-chr14:69253853..69256303,2	MCF-7	breast:
37	chr14:69232699..69236940-chr14:69253332..69256719,3	K562	blood:
38	chr14:68986084..68990937-chr14:69249749..69255560,7	MCF-7	breast:
39	chr14:68849181..68851352-chr14:69252544..69254272,2	MCF-7	breast:
40	chr14:69135163..69138433-chr14:69253381..69256007,3	MCF-7	breast:
41	chr14:69041655..69043328-chr14:69251823..69254372,2	MCF-7	breast:
42	chr14:68931679..68940045-chr14:69251548..69257130,11	MCF-7	breast:
43	chr14:69135342..69138220-chr14:69251812..69254246,3	MCF-7	breast:
44	chr14:69128066..69130361-chr14:69254081..69256689,3	MCF-7	breast:
45	chr14:68779162..68780935-chr14:69252607..69255132,2	MCF-7	breast:
46	chr14:69050198..69051836-chr14:69253658..69256405,2	MCF-7	breast:
47	chr14:69175164..69177476-chr14:69251993..69254920,2	MCF-7	breast:
48	chr14:68875187..68876826-chr14:69253735..69255769,2	MCF-7	breast:
49	chr14:69029510..69035367-chr14:69250877..69256211,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267598	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000259038	Chromatin interaction
ENSG00000182185	Chromatin interaction
ENSG00000141526	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11158762	0.80[JPT][hapmap]
rs11158763	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12434551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12435329	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12889006	1.00[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1465788	0.80[JPT][hapmap]
rs1595260	0.80[JPT][hapmap]
rs2236262	1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34489253	0.80[AMR][1000 genomes]
rs3825568	0.92[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4899257	0.91[AMR][1000 genomes]
rs7146217	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs7146491	0.90[ASN][1000 genomes]
rs747854	0.83[GIH][hapmap]
rs8022092	0.80[AMR][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

Variant related diseases (count:1)

Disease	PMID	Source
Multiple sclerosis	21833088	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4902647	ZFP36L1	Cis_1M	lymphoblastoid	RTeQTL
rs4902647	ZFP36L1	cis	uninvolved skin	skin_eQTL
rs4902647	ZFP36L1	cis	normal skin	skin_eQTL
rs4902647	ZFP36L1	cis	lesional skin	skin_eQTL
rs4902647	MAX	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:69248200-69255800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:69248400-69255800	Weak transcription	Brain Anterior Caudate	brain
3	chr14:69248600-69255000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr14:69248600-69255800	Weak transcription	Brain Angular Gyrus	brain
5	chr14:69248800-69255200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr14:69249000-69255200	Weak transcription	Fetal Brain Male	brain
7	chr14:69249400-69254200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr14:69249600-69255200	Weak transcription	Dnd41	blood
9	chr14:69251000-69254200	Enhancers	HUVEC	blood vessel
10	chr14:69252200-69254400	Genic enhancers	Fetal Stomach	stomach
11	chr14:69252200-69255200	Genic enhancers	Fetal Intestine Small	intestine
12	chr14:69252400-69254400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr14:69252400-69255600	Enhancers	HepG2	liver
14	chr14:69252600-69254400	Genic enhancers	Fetal Muscle Trunk	muscle
15	chr14:69252600-69254800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr14:69252600-69255400	Enhancers	Fetal Heart	heart
17	chr14:69252800-69254800	Enhancers	Small Intestine	intestine
18	chr14:69253000-69254200	Genic enhancers	Fetal Lung	lung
19	chr14:69253000-69254400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr14:69253000-69254600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr14:69253000-69254600	Genic enhancers	Thymus	Thymus
22	chr14:69253000-69255200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr14:69253000-69255400	Genic enhancers	Primary B cells from peripheral blood	blood
24	chr14:69253200-69254400	Genic enhancers	Colonic Mucosa	Colon
25	chr14:69253200-69254400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
26	chr14:69253200-69254600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr14:69253200-69254600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr14:69253200-69254600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr14:69253200-69255000	Genic enhancers	Fetal Intestine Large	intestine
30	chr14:69253200-69255000	Genic enhancers	Fetal Thymus	thymus
31	chr14:69253200-69255200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr14:69253200-69255200	Genic enhancers	Placenta	Placenta
33	chr14:69253400-69254200	Genic enhancers	Primary B cells from cord blood	blood
34	chr14:69253400-69254400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr14:69253400-69254400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr14:69253400-69254400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr14:69253400-69254400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr14:69253400-69254400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr14:69253400-69254400	Enhancers	Right Atrium	heart
40	chr14:69253400-69254400	Genic enhancers	Spleen	Spleen
41	chr14:69253400-69254400	Genic enhancers	NHEK	skin
42	chr14:69253400-69254600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr14:69253400-69254600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr14:69253400-69254800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr14:69253400-69255200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr14:69253400-69255200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr14:69253400-69255200	Genic enhancers	Rectal Mucosa Donor 31	rectum
48	chr14:69253400-69255800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
49	chr14:69253600-69254200	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr14:69253600-69254200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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