Variant report

Variant	rs3742521
Chromosome Location	chr14:24906515-24906516
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:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:86510736..86512515-chr14:24906135..24907852,2	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	chr14:24777377..24780208-chr14:24906174..24908907,2	K562	blood:
5	chr14:24816528..24849574-chr14:24893305..24914155,145	MCF-7	breast:
6	chr14:24789439..24822082-chr14:24898039..24913135,99	MCF-7	breast:
7	chr14:24905848..24906564-chr14:25147935..25148721,2	MCF-7	breast:
8	chr14:24791358..24808812-chr14:24895309..24913599,55	K562	blood:
9	chr14:24704769..24706424-chr14:24904914..24907599,2	MCF-7	breast:
10	chr14:24802504..24803506-chr14:24905350..24906802,10	MCF-7	breast:
11	chr14:24865931..24867961-chr14:24906005..24908600,2	MCF-7	breast:
12	chr14:24864264..24865862-chr14:24905132..24908041,2	MCF-7	breast:
13	chr14:24787946..24789966-chr14:24905926..24907648,2	K562	blood:
14	chr14:24802185..24803542-chr14:24905287..24906769,13	MCF-7	breast:
15	chr14:24710779..24713776-chr14:24905054..24908249,5	MCF-7	breast:
16	chr14:24827418..24850855-chr14:24894884..24913772,127	MCF-7	breast:
17	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
18	chr14:24483262..24483795-chr14:24906005..24906586,2	K562	blood:
19	chr14:24710058..24711559-chr14:24906353..24908721,2	MCF-7	breast:
20	chr14:24834374..24835487-chr14:24905615..24906819,12	MCF-7	breast:
21	chr14:24774877..24777510-chr14:24906503..24909154,3	MCF-7	breast:
22	chr14:24802540..24803456-chr14:24905606..24906604,3	K562	blood:
23	chr14:24775299..24777826-chr14:24904340..24907258,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000157379	Chromatin interaction
ENSG00000213903	Chromatin interaction
ENSG00000207141	Chromatin interaction
ENSG00000150687	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000196943	Chromatin interaction
ENSG00000213906	Chromatin interaction
ENSG00000100968	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000129465	Chromatin interaction
ENSG00000272658	Chromatin interaction
ENSG00000136305	Chromatin interaction
ENSG00000100938	Chromatin interaction
ENSG00000258973	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10083368	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10083369	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10083379	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10083382	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10083509	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10129168	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10129753	0.97[ASN][1000 genomes]
rs10133116	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10133998	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10140911	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10144287	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10146995	0.99[ASN][1000 genomes]
rs1043831	0.83[ASW][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap]
rs1043839	0.83[ASW][hapmap];0.87[JPT][hapmap]
rs11158703	0.83[ASW][hapmap];0.87[JPT][hapmap]
rs11158705	0.83[ASW][hapmap];0.87[JPT][hapmap]
rs11538255	1.00[ASN][1000 genomes]
rs11538256	1.00[ASN][1000 genomes]
rs11628143	0.83[ASW][hapmap];0.87[JPT][hapmap]
rs12433369	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12882878	0.87[JPT][hapmap]
rs12884447	0.87[JPT][hapmap]
rs17103735	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103743	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17103869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17103960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17104012	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1951137	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs1956896	0.87[JPT][hapmap]
rs1956898	0.83[ASW][hapmap];0.87[JPT][hapmap]
rs1956903	0.83[AFR][1000 genomes]
rs1956904	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs1956921	0.88[CHB][hapmap];0.86[JPT][hapmap]
rs2073335	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2273628	0.83[ASW][hapmap];0.87[JPT][hapmap]
rs2332333	0.87[JPT][hapmap]
rs3211056	0.87[JPT][hapmap]
rs3742522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809	0.83[ASW][hapmap];0.87[JPT][hapmap]
rs3814810	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4981518	0.86[JPT][hapmap]
rs4981519	0.87[JPT][hapmap]
rs4982913	0.83[ASW][hapmap];0.86[JPT][hapmap]
rs4982914	0.87[JPT][hapmap]
rs4982917	0.86[JPT][hapmap]
rs4982920	0.85[JPT][hapmap]
rs55953421	0.83[ASN][1000 genomes]
rs57120899	0.84[ASN][1000 genomes]
rs57259303	0.91[ASN][1000 genomes]
rs59448251	0.94[ASN][1000 genomes]
rs60777821	0.84[ASN][1000 genomes]
rs712487	0.83[ASW][hapmap];0.87[JPT][hapmap]
rs7142374	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7143327	0.87[JPT][hapmap]
rs7144118	0.87[JPT][hapmap]
rs7149743	0.87[JPT][hapmap]
rs7157349	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs73593291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73593299	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737245	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs737246	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs737247	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs737248	0.87[JPT][hapmap]
rs9323503	0.84[ASN][1000 genomes]
rs966493	0.83[ASW][hapmap];0.87[JPT][hapmap]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3742521	SDR39U1	cis	Muscle Skeletal	GTEx
rs3742521	SDR39U1	cis	lymphoblastoid	seeQTL

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	chr14:24901000-24906600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr14:24901000-24906800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr14:24901000-24908600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr14:24901400-24906800	Weak transcription	K562	blood
9	chr14:24901400-24910200	Strong transcription	Aorta	Aorta
10	chr14:24901600-24906800	Weak transcription	Fetal Brain Male	brain
11	chr14:24901600-24907200	Weak transcription	Hela-S3	cervix
12	chr14:24901600-24909800	Weak transcription	Fetal Heart	heart
13	chr14:24901600-24910400	Strong transcription	Placenta Amnion	Placenta Amnion
14	chr14:24901800-24909000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr14:24901800-24910000	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr14:24902000-24906600	Strong transcription	Esophagus	oesophagus
17	chr14:24902000-24909200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr14:24902200-24909400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr14:24902400-24906800	Weak transcription	Brain Germinal Matrix	brain
20	chr14:24902400-24907200	Weak transcription	Fetal Brain Female	brain
21	chr14:24902400-24908600	Strong transcription	HMEC	breast
22	chr14:24902400-24909400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr14:24902400-24909800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr14:24902400-24910200	Strong transcription	A549	lung
25	chr14:24902400-24910600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr14:24902800-24906800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr14:24903000-24910000	Weak transcription	Psoas Muscle	Psoas
28	chr14:24903000-24910000	Strong transcription	NHEK	skin
29	chr14:24903400-24906800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr14:24903400-24909600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr14:24903600-24906800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr14:24903800-24908600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr14:24903800-24909000	Strong transcription	Pancreas	Pancrea
34	chr14:24904000-24907200	Genic enhancers	Dnd41	blood
35	chr14:24904000-24908200	Genic enhancers	Liver	Liver
36	chr14:24904200-24910200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
37	chr14:24904400-24907800	Genic enhancers	Stomach Smooth Muscle	stomach
38	chr14:24904400-24910400	Genic enhancers	Adipose Nuclei	Adipose
39	chr14:24904600-24908200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
40	chr14:24904600-24910400	Strong transcription	Fetal Lung	lung
41	chr14:24904800-24907000	Genic enhancers	GM12878-XiMat	blood
42	chr14:24904800-24907200	Genic enhancers	Placenta	Placenta
43	chr14:24904800-24907600	Genic enhancers	HUVEC	blood vessel
44	chr14:24904800-24910400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr14:24905000-24908600	Strong transcription	Gastric	stomach
46	chr14:24905200-24906600	Genic enhancers	Brain Inferior Temporal Lobe	brain
47	chr14:24905200-24907200	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr14:24905200-24907200	Genic enhancers	Fetal Muscle Trunk	muscle
49	chr14:24905200-24907400	Genic enhancers	Primary B cells from cord blood	blood
50	chr14:24905200-24907800	Genic enhancers	Fetal Muscle Leg	muscle

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