Variant report

Variant	rs9864406
Chromosome Location	chr3:49352619-49352620
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49352460-49353427	GM12892	blood:	n/a	n/a
2	POLR2A	chr3:49352451-49353548	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:49352522-49353285	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:49352427-49353325	GM12892	blood:	n/a	n/a
5	POLR2A	chr3:49352444-49353451	GM12892	blood:	n/a	n/a
6	STAT3	chr3:49352557-49352757	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
USP4	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11552724	1.00[JPT][hapmap]
rs11707940	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11709788	0.98[ASN][1000 genomes]
rs11720964	0.86[ASN][1000 genomes]
rs11920251	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12497569	0.95[ASN][1000 genomes]
rs12715435	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13077498	0.85[CHD][hapmap]
rs13077723	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13078949	0.86[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs1865741	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2230929	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304442	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34142492	0.93[ASN][1000 genomes]
rs34366700	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34514189	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34566463	0.91[MKK][hapmap]
rs34567776	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34915642	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35446411	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35869135	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4410472	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4554002	0.93[ASN][1000 genomes]
rs4855842	0.85[CHB][hapmap]
rs4955431	0.95[ASN][1000 genomes]
rs56038006	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67882627	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6795772	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs73086105	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7640903	0.93[ASN][1000 genomes]
rs9814987	0.91[MKK][hapmap]
rs9818758	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9847839	0.91[MKK][hapmap]
rs9850917	1.00[JPT][hapmap]
rs9863142	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873994	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9874474	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9883409	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][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
rs9864406	CELSR3	cis	cerebellum	SCAN
rs9864406	NICN1	cis	cerebellum	SCAN
rs9864406	RNF123	cis	parietal	SCAN
rs9864406	USP4	cis	multi-tissue	Pritchard
rs9864406	C3orf62	cis	parietal	SCAN
rs9864406	C3orf62	cis	cerebellum	SCAN
rs9864406	UQCRC1	cis	parietal	SCAN
rs9864406	NDUFAF3	cis	parietal	SCAN
rs9864406	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9864406	GPX1	cis	parietal	SCAN
rs9864406	NBEAL2	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	chr3:49314800-49355400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:49314800-49364800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:49315200-49373600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:49315200-49375000	Strong transcription	Fetal Stomach	stomach
6	chr3:49315400-49370400	Strong transcription	Fetal Thymus	thymus
7	chr3:49316200-49370200	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:49317200-49371800	Strong transcription	Fetal Intestine Small	intestine
9	chr3:49317400-49369400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:49317400-49370600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:49319200-49374800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:49319600-49371800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:49320200-49375000	Strong transcription	Thymus	Thymus
14	chr3:49320800-49368000	Strong transcription	Primary T cells from cord blood	blood
15	chr3:49321800-49373600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:49326800-49373400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr3:49326800-49375000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:49332600-49354400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:49333600-49369600	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr3:49335000-49365200	Strong transcription	Spleen	Spleen
21	chr3:49335000-49369400	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:49335000-49375000	Strong transcription	Placenta	Placenta
23	chr3:49335200-49365200	Strong transcription	Lung	lung
24	chr3:49335200-49369800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr3:49335200-49375200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr3:49335400-49365200	Strong transcription	Fetal Muscle Leg	muscle
27	chr3:49336200-49354200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:49336200-49365600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:49338200-49361600	Weak transcription	Stomach Mucosa	stomach
30	chr3:49338200-49375000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:49348200-49358200	Weak transcription	Psoas Muscle	Psoas
32	chr3:49348400-49361200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:49348600-49354200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:49348600-49361800	Weak transcription	Fetal Brain Male	brain
35	chr3:49348800-49354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:49348800-49354200	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:49348800-49358200	Weak transcription	A549	lung
38	chr3:49349000-49353000	Weak transcription	Aorta	Aorta
39	chr3:49349000-49353000	Weak transcription	Gastric	stomach
40	chr3:49349000-49353000	Weak transcription	Pancreas	Pancrea
41	chr3:49349000-49354200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr3:49349000-49354200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr3:49349000-49354200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:49349000-49354400	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:49349000-49358000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr3:49349000-49358000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr3:49349000-49359600	Weak transcription	Hela-S3	cervix
48	chr3:49349000-49362400	Weak transcription	Fetal Heart	heart
49	chr3:49349200-49353800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr3:49349200-49354200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links