Variant report

Variant	rs2277489
Chromosome Location	chr14:24905548-24905549
allele	A/G
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24778484..24781723-chr14:24903121..24905574,3	MCF-7	breast:
2	chr14:24801605..24806320-chr14:24904693..24909744,5	K562	blood:
3	chr14:24766500..24769318-chr14:24904767..24907330,3	MCF-7	breast:
4	chr14:24816528..24849574-chr14:24893305..24914155,145	MCF-7	breast:
5	chr14:24789439..24822082-chr14:24898039..24913135,99	MCF-7	breast:
6	chr14:24791358..24808812-chr14:24895309..24913599,55	K562	blood:
7	chr14:24704769..24706424-chr14:24904914..24907599,2	MCF-7	breast:
8	chr14:24802504..24803506-chr14:24905350..24906802,10	MCF-7	breast:
9	chr14:24707993..24709532-chr14:24903612..24905899,2	MCF-7	breast:
10	chr14:24655837..24658282-chr14:24904503..24906148,2	K562	blood:
11	chr14:24864264..24865862-chr14:24905132..24908041,2	MCF-7	breast:
12	chr14:24802185..24803542-chr14:24905287..24906769,13	MCF-7	breast:
13	chr14:24710779..24713776-chr14:24905054..24908249,5	MCF-7	breast:
14	chr14:24827418..24850855-chr14:24894884..24913772,127	MCF-7	breast:
15	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
16	chr14:24801279..24801856-chr14:24905358..24906438,3	K562	blood:
17	chr14:24769037..24771886-chr14:24904413..24906460,2	MCF-7	breast:
18	chr14:24777042..24777554-chr14:24905532..24906095,2	MCF-7	breast:
19	chr14:24775299..24777826-chr14:24904340..24907258,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000207141	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000100938	Chromatin interaction
ENSG00000129465	Chromatin interaction
ENSG00000100968	Chromatin interaction
ENSG00000196943	Chromatin interaction
ENSG00000136305	Chromatin interaction
ENSG00000213903	Chromatin interaction
ENSG00000157379	Chromatin interaction
ENSG00000258973	Chromatin interaction
ENSG00000213906	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10083382	0.84[MEX][hapmap]
rs10083509	0.84[MEX][hapmap]
rs10143987	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1043831	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1043839	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11158703	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11158704	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11158705	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11158706	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11158707	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11621453	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11621715	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11626161	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11627132	0.80[AMR][1000 genomes]
rs11628143	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12433369	0.89[ASN][1000 genomes]
rs12433402	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12879887	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12882878	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12884447	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12897925	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1473725	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17103743	0.84[MEX][hapmap]
rs17184822	1.00[CEU][hapmap];0.88[TSI][hapmap]
rs1951123	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1956893	0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1956896	1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1956898	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1956899	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1956901	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1956903	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1956904	0.92[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2273628	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2332333	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2332334	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3211056	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3809	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4278673	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4290409	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4400972	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4433735	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4981518	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4981519	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4981521	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4981522	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4981523	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4981524	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4982913	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4982914	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4982916	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4982917	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4982919	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4982920	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs712487	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7143327	0.92[CEU][hapmap];0.90[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7144118	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7148891	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7149743	0.84[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7151530	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs737248	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8008300	0.82[ASN][1000 genomes]
rs8015535	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs966493	0.92[CEU][hapmap];0.91[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2277489	SDR39U1	cis	lymphoblastoid	seeQTL
rs2277489	FAM158A	cis	lymphoblastoid	GTEx
rs2277489	SDR39U1	cis	Muscle Skeletal	GTEx
rs2277489	C14orf124	Cis_1M	lymphoblastoid	RTeQTL
rs2277489	JPH4	cis	parietal	SCAN
rs2277489	SDR39U1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24900200-24906600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr14:24900200-24911000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr14:24900600-24907800	Weak transcription	Small Intestine	intestine
4	chr14:24900600-24910600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr14:24901000-24905600	Weak transcription	Brain Angular Gyrus	brain
6	chr14:24901000-24906200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr14:24901000-24906600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr14:24901000-24906800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr14:24901000-24908600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr14:24901200-24905800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr14:24901200-24906000	Strong transcription	Thymus	Thymus
12	chr14:24901400-24905800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr14:24901400-24906200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr14:24901400-24906400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr14:24901400-24906800	Weak transcription	K562	blood
16	chr14:24901400-24910200	Strong transcription	Aorta	Aorta
17	chr14:24901600-24905600	Strong transcription	Ovary	ovary
18	chr14:24901600-24905800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr14:24901600-24905800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr14:24901600-24905800	Strong transcription	Rectal Smooth Muscle	rectum
21	chr14:24901600-24906200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr14:24901600-24906200	Strong transcription	Lung	lung
23	chr14:24901600-24906800	Weak transcription	Fetal Brain Male	brain
24	chr14:24901600-24907200	Weak transcription	Hela-S3	cervix
25	chr14:24901600-24909800	Weak transcription	Fetal Heart	heart
26	chr14:24901600-24910400	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr14:24901800-24905600	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr14:24901800-24905600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr14:24901800-24909000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr14:24901800-24910000	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr14:24902000-24905600	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr14:24902000-24905600	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr14:24902000-24905600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr14:24902000-24905600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr14:24902000-24905600	Strong transcription	Fetal Intestine Large	intestine
36	chr14:24902000-24905600	Strong transcription	NH-A	brain
37	chr14:24902000-24905800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr14:24902000-24905800	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr14:24902000-24906200	Strong transcription	Spleen	Spleen
40	chr14:24902000-24906600	Strong transcription	Esophagus	oesophagus
41	chr14:24902000-24909200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr14:24902200-24909400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr14:24902400-24905600	Strong transcription	Fetal Stomach	stomach
44	chr14:24902400-24906200	Strong transcription	Duodenum Mucosa	Duodenum
45	chr14:24902400-24906800	Weak transcription	Brain Germinal Matrix	brain
46	chr14:24902400-24907200	Weak transcription	Fetal Brain Female	brain
47	chr14:24902400-24908600	Strong transcription	HMEC	breast
48	chr14:24902400-24909400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr14:24902400-24909800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr14:24902400-24910200	Strong transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links