Variant report

Variant	rs4680405
Chromosome Location	chr3:151110888-151110889
allele	A/G
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	CHD2	chr3:151110847-151111653	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAFK	chr3:151110811-151111544	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
MED12L	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10513398	0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs10513399	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs10935840	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10935841	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10935842	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10935843	0.87[EUR][1000 genomes]
rs10935844	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs10935845	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs11707416	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11708287	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11708767	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11709550	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11713504	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11717169	0.86[EUR][1000 genomes]
rs11923424	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12485508	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12488803	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12489121	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12490051	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490184	0.86[EUR][1000 genomes]
rs12492266	0.86[EUR][1000 genomes]
rs12493628	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12497065	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12497089	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs12498042	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1491974	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17204501	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17204508	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17204515	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17204536	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17283010	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17283038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17283052	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17283059	0.84[EUR][1000 genomes]
rs17504	0.94[AFR][1000 genomes]
rs2276764	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2276765	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs3732765	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs3732769	0.83[YRI][hapmap]
rs3821663	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4679817	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4680400	0.87[EUR][1000 genomes]
rs4680406	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4680408	0.86[EUR][1000 genomes]
rs57335550	0.86[EUR][1000 genomes]
rs57781984	0.86[EUR][1000 genomes]
rs59605118	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60105866	0.86[EUR][1000 genomes]
rs6787801	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs67886110	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6798637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6803771	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs73159907	0.88[EUR][1000 genomes]
rs73159908	0.88[EUR][1000 genomes]
rs73159915	0.86[EUR][1000 genomes]
rs73159920	0.86[EUR][1000 genomes]
rs7612010	0.85[ASN][1000 genomes]
rs765281	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289836	0.83[YRI][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	nsv829757	chr3:151044880-151226442	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1000355	chr3:151108859-151243835	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4680405	P2RY12	cis	Adipose Subcutaneous	GTEx
rs4680405	P2RY12	cis	lung	GTEx

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:151064600-151112400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:151065600-151115200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:151069400-151129800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:151075600-151136400	Weak transcription	Fetal Brain Female	brain
5	chr3:151087600-151116000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:151090200-151142400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:151095400-151111000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:151096000-151129000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:151096600-151112400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:151098800-151143400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:151102200-151148600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:151102600-151113600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr3:151102600-151132000	Weak transcription	Brain Angular Gyrus	brain
14	chr3:151102800-151113400	Weak transcription	NHLF	lung
15	chr3:151102800-151136400	Weak transcription	Brain Substantia Nigra	brain
16	chr3:151102800-151150600	Weak transcription	Brain Anterior Caudate	brain
17	chr3:151103000-151111200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:151104000-151112400	Weak transcription	NHDF-Ad	bronchial
19	chr3:151104200-151139600	Weak transcription	Dnd41	blood
20	chr3:151104400-151113400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr3:151106000-151130800	Weak transcription	Fetal Intestine Small	intestine
22	chr3:151106000-151134200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:151106000-151154600	Weak transcription	Fetal Muscle Leg	muscle
24	chr3:151106200-151122000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:151106200-151128000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:151106200-151131200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:151106400-151121400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr3:151106400-151121400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr3:151109000-151111400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr3:151109000-151115200	Weak transcription	Placenta	Placenta
31	chr3:151109200-151113200	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr3:151109400-151112200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:151110000-151116000	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:151110400-151112600	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr3:151110800-151111000	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr3:151110800-151111000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr3:151110800-151111000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
38	chr3:151110800-151111000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr3:151110800-151111000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr3:151110800-151112800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links