Variant report

Variant	rs12715434
Chromosome Location	chr3:49295025-49295026
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr3:49295011-49295061	ovcar-3	ovarian:	n/a
2	chr3:49295011-49295061	U87	brain:	n/a
3	chr3:49295011-49295061	AG04449	skin:	fetal
4	chr3:49295011-49295061	HepG2	liver:	n/a
5	chr3:49295011-49295061	K562	blood:	n/a
6	chr3:49295011-49295061	ECC-1	luminal epithelium:	n/a
7	chr3:49295011-49295061	HRPEpiC	eye:	n/a
8	chr3:49295011-49295061	GM06990	blood:	n/a
9	chr3:49295011-49295061	LNCaP	prostate:	n/a
10	chr3:49295011-49295061	HNPCEpiC	eye:	n/a
11	chr3:49295011-49295061	GM12878	blood:	n/a
12	chr3:49295011-49295061	BJ	skin:	n/a
13	chr3:49295011-49295061	HAEpiC	amniotic membrane:	n/a
14	chr3:49295011-49295061	AG09309	skin:	n/a
15	chr3:49295011-49295061	HL-60	blood:	n/a
16	chr3:49295011-49295061	T-47D	breast:	n/a
17	chr3:49295011-49295061	MCF-7	breast:	n/a
18	chr3:49295011-49295061	Caco-2	colon:	n/a
19	chr3:49295011-49295061	Jurkat	blood:	n/a
20	chr3:49295011-49295061	GM19239	blood:	n/a
21	chr3:49295011-49295061	SK-N-MC	brain:	n/a
22	chr3:49295011-49295061	HMEC	breast:	n/a
23	chr3:49295011-49295061	NHBE	bronchial:	n/a
24	chr3:49295011-49295061	HCF	heart:	n/a
25	chr3:49295011-49295061	HCPEpiC	choroid plexus:	n/a
26	chr3:49295011-49295061	PrEC	prostate:	n/a
27	chr3:49295011-49295061	ProgFib	skin:	n/a
28	chr3:49295011-49295061	HIPEpiC	eye:	n/a
29	chr3:49295011-49295061	IMR90	lung:	fetal
30	chr3:49295011-49295061	A549	lung:	n/a
31	chr3:49295011-49295061	NT2-D1	testis:	n/a
32	chr3:49295011-49295061	HRCEpiC	kidney:	n/a
33	chr3:49295011-49295061	HUVEC	blood vessel:	n/a
34	chr3:49295011-49295061	HRE	kidney:	n/a
35	chr3:49295011-49295061	SK-N-SH	brain:	n/a
36	chr3:49295011-49295061	BE2_C	brain:	n/a
37	chr3:49295011-49295061	NB4	blood:	n/a
38	chr3:49295011-49295061	HEEpiC	esophagus:	n/a
39	chr3:49295011-49295061	GM12892	blood:	n/a
40	chr3:49295011-49295061	Hela-S3	cervix:	n/a
41	chr3:49295011-49295061	HCM	heart:	n/a
42	chr3:49295011-49295061	HPAEpiC	pulmonary alveolar:	n/a
43	chr3:49295011-49295061	SKMC	muscle:	n/a
44	chr3:49295011-49295061	PANC-1	pancreas:	n/a
45	chr3:49295011-49295061	SK-N-SH_RA	brain:	n/a
46	chr3:49295011-49295061	Hepatocyte	liver:	n/a
47	chr3:49295011-49295061	H1-hESC	embryonic stem cell:	embryo
48	chr3:49295011-49295061	GM12891	blood:	n/a
49	chr3:49295011-49295061	RPTEC	kidney:	n/a
50	chr3:49295011-49295061	AG09319	gingival:	n/a

No data

Variant related genes	Relation type
ENSG00000225399	CpG island

Extended variants
information (count: 56 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10049462	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10154895	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11552724	0.91[EUR][1000 genomes]
rs11706052	0.81[EUR][1000 genomes]
rs11706189	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11710247	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11713297	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11718982	0.86[EUR][1000 genomes]
rs11719220	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11720460	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12493284	0.83[ASN][1000 genomes]
rs12629637	0.97[ASN][1000 genomes]
rs12715435	0.81[AFR][1000 genomes]
rs13068038	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13072554	0.80[EUR][1000 genomes]
rs13077498	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13096406	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2304442	0.86[ASN][1000 genomes]
rs34326553	0.87[EUR][1000 genomes]
rs34343820	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34566463	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34784192	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35060561	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35108630	0.81[EUR][1000 genomes]
rs35174559	0.92[ASN][1000 genomes]
rs35185152	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35673421	0.89[EUR][1000 genomes]
rs4410472	0.91[ASN][1000 genomes]
rs5030795	0.91[EUR][1000 genomes]
rs55921200	0.81[EUR][1000 genomes]
rs56306491	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs66991555	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67286839	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67831908	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71324939	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73084135	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7614738	0.83[ASN][1000 genomes]
rs7638154	0.87[ASN][1000 genomes]
rs9311439	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9814987	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9826525	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9828310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9835439	0.89[EUR][1000 genomes]
rs9837237	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9837625	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9847839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850917	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9855123	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9862483	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9870030	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9874474	0.86[ASN][1000 genomes]
rs9880088	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9880309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9883409	0.86[ASN][1000 genomes]
rs9990153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1008750	chr3:49208815-49362401	Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12715434	WDR6	cis	Artery Tibial	GTEx
rs12715434	WDR6	cis	Adipose Subcutaneous	GTEx
rs12715434	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs12715434	WDR6	cis	Esophagus Mucosa	GTEx
rs12715434	WDR6	cis	Whole Blood	GTEx
rs12715434	USP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49276400-49306400	Weak transcription	Spleen	Spleen
2	chr3:49276600-49304000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:49282600-49299000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:49282600-49303200	Weak transcription	Left Ventricle	heart
5	chr3:49286400-49304000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:49286400-49313600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:49290600-49303400	Weak transcription	Brain Angular Gyrus	brain
8	chr3:49292200-49295400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:49292800-49306800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:49293000-49313400	Weak transcription	HSMM	muscle
11	chr3:49293200-49295200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr3:49293600-49304000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:49293600-49306400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:49293800-49305400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr3:49293800-49306400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr3:49293800-49307000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:49293800-49308400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr3:49294000-49296400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:49294000-49306600	Weak transcription	Placenta	Placenta
20	chr3:49294000-49308400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:49294200-49297600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr3:49294200-49303400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:49294400-49304000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:49294600-49303200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr3:49294600-49303400	Weak transcription	Fetal Muscle Leg	muscle
26	chr3:49294600-49304000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:49294800-49297800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:49294800-49298000	Weak transcription	Adipose Nuclei	Adipose
29	chr3:49294800-49303200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:49294800-49306800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:49294800-49313400	Weak transcription	NHLF	lung
32	chr3:49295000-49297400	Weak transcription	Fetal Intestine Large	intestine
33	chr3:49295000-49297600	Weak transcription	Fetal Intestine Small	intestine
34	chr3:49295000-49297800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr3:49295000-49303400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:49295000-49303400	Weak transcription	Rectal Smooth Muscle	rectum
37	chr3:49295000-49303400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr3:49295000-49304000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:49295000-49304000	Weak transcription	Fetal Stomach	stomach
40	chr3:49295000-49304200	Weak transcription	Osteobl	bone
41	chr3:49295000-49306600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:49295000-49313200	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links