Variant report

Variant	rs9874474
Chromosome Location	chr3:49326178-49326179
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10049462	0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10865954	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11130184	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11552724	1.00[JPT][hapmap]
rs11706189	1.00[JPT][hapmap]
rs11707940	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11713297	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11715581	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11719220	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs11920267	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12490393	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12493001	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs12493284	0.97[ASN][1000 genomes]
rs12629637	0.83[ASN][1000 genomes]
rs12629759	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12631989	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12637576	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12715434	0.86[ASN][1000 genomes]
rs12715435	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13068038	0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13077498	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13077723	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2117938	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2230929	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2304442	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs34343820	0.86[ASN][1000 genomes]
rs34366700	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34514189	0.92[EUR][1000 genomes]
rs34566463	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap]
rs34567776	0.93[EUR][1000 genomes]
rs34915642	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35060561	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs35174559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs35446411	0.91[EUR][1000 genomes]
rs35673421	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs35869135	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3774799	0.89[ASN][1000 genomes]
rs4279134	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4410472	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4513485	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4521268	0.82[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4955410	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4955418	1.00[JPT][hapmap]
rs4955419	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4955420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4955432	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs5030795	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs56038006	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6779394	1.00[JPT][hapmap]
rs67831908	0.86[ASN][1000 genomes]
rs6784111	1.00[JPT][hapmap]
rs67882627	0.92[EUR][1000 genomes]
rs73086105	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7374375	0.90[ASN][1000 genomes]
rs7614738	0.80[ASN][1000 genomes]
rs7638154	0.84[ASN][1000 genomes]
rs7652746	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9311439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9814987	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap]
rs9818758	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs9828310	0.86[ASN][1000 genomes]
rs9837237	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9837625	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9840050	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs9847839	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.95[MKK][hapmap];0.86[ASN][1000 genomes]
rs9850917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9863142	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9864406	0.93[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9873994	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9880088	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs9880309	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9883409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990153	0.85[CHD][hapmap];1.00[JPT][hapmap];0.86[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs9874474	CELSR3	cis	cerebellum	SCAN
rs9874474	NDUFAF3	cis	parietal	SCAN
rs9874474	NICN1	cis	cerebellum	SCAN
rs9874474	NBEAL2	cis	cerebellum	SCAN
rs9874474	GPX1	cis	parietal	SCAN
rs9874474	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9874474	RNF123	cis	parietal	SCAN
rs9874474	C3orf62	cis	parietal	SCAN
rs9874474	UQCRC1	cis	parietal	SCAN
rs9874474	RBM6	Cis_1M	lymphoblastoid	RTeQTL
rs9874474	C3orf62	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49312600-49375800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49313200-49326200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49313200-49349400	Strong transcription	Dnd41	blood
4	chr3:49313600-49349200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:49314800-49334600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:49314800-49355400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:49314800-49364800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:49315200-49327600	Strong transcription	Placenta	Placenta
9	chr3:49315200-49349600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr3:49315200-49349600	Strong transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:49315200-49352600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:49315200-49373600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr3:49315200-49375000	Strong transcription	Fetal Stomach	stomach
14	chr3:49315400-49327600	Strong transcription	GM12878-XiMat	blood
15	chr3:49315400-49335800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:49315400-49370400	Strong transcription	Fetal Thymus	thymus
17	chr3:49315600-49332400	Strong transcription	Brain Hippocampus Middle	brain
18	chr3:49315800-49333000	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr3:49315800-49349200	Strong transcription	Fetal Brain Female	brain
20	chr3:49316200-49334600	Strong transcription	Fetal Muscle Trunk	muscle
21	chr3:49316200-49370200	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr3:49316400-49328600	Strong transcription	Fetal Lung	lung
23	chr3:49316600-49340200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr3:49317200-49334200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:49317200-49349400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr3:49317200-49371800	Strong transcription	Fetal Intestine Small	intestine
27	chr3:49317400-49331200	Strong transcription	Adipose Nuclei	Adipose
28	chr3:49317400-49332200	Strong transcription	Right Ventricle	heart
29	chr3:49317400-49334200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:49317400-49334200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:49317400-49334200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:49317400-49334200	Strong transcription	Fetal Muscle Leg	muscle
33	chr3:49317400-49334200	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr3:49317400-49334600	Strong transcription	Left Ventricle	heart
35	chr3:49317400-49349200	Strong transcription	Fetal Intestine Large	intestine
36	chr3:49317400-49349600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:49317400-49369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:49317400-49370600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:49317600-49331600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:49319200-49333600	Strong transcription	HSMMtube	muscle
41	chr3:49319200-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:49319400-49333000	Strong transcription	Primary hematopoietic stem cells	blood
43	chr3:49319400-49349600	Strong transcription	Liver	Liver
44	chr3:49319600-49332600	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:49319600-49334200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:49319600-49344000	Strong transcription	Osteobl	bone
47	chr3:49319600-49349400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr3:49319600-49371800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:49319800-49349200	Strong transcription	Brain Germinal Matrix	brain
50	chr3:49319800-49349400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links