Variant report

Variant	rs4887062
Chromosome Location	chr15:78837801-78837802
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs11630349	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11632604	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11636131	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11858230	0.91[CEU][hapmap];0.84[CHB][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12591557	0.92[CEU][hapmap];0.86[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12594391	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12900612	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12900783	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12902493	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12903129	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12906284	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12906846	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12906951	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12907169	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12907425	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12907966	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910100	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12910289	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12910726	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910969	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12910978	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12912022	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12912673	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12913173	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12914694	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12915366	0.88[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12915428	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12915652	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12916483	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12916999	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1504545	0.96[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1504546	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1504548	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17407257	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1847530	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1979905	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1979906	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1979907	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1979908	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2292117	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28392948	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28438420	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2869055	0.87[EUR][1000 genomes]
rs2869544	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3813571	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3813572	0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4243083	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4275821	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs4886571	0.96[CEU][hapmap];0.86[CHB][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4886572	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4887063	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4887064	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5022780	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs555018	0.80[CEU][hapmap]
rs55690619	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56007453	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs588765	0.83[CEU][hapmap]
rs601079	0.81[CEU][hapmap]
rs62008174	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62008193	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62008194	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7164030	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7173512	0.81[CEU][hapmap];0.82[YRI][hapmap]
rs8025429	0.96[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8053	0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs880395	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs905740	0.96[CEU][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs952215	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs952216	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]

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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh 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	122 gene(s)	inside rSNPs	diseases
2	nsv1038816	chr15:78796434-78881087	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4887062	CHRNA5	cis	Muscle Skeletal	GTEx
rs4887062	CHRNA3	cis	Muscle Skeletal	GTEx
rs4887062	CHRNA5	cis	Esophagus Mucosa	GTEx
rs4887062	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs4887062	RP11-650L12.2	cis	Esophagus Mucosa	GTEx
rs4887062	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs4887062	RP11-650L12.2	cis	Nerve Tibial	GTEx
rs4887062	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs4887062	CHRNA5	cis	Nerve Tibial	GTEx
rs4887062	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs4887062	CHRNA5	cis	lung	GTEx
rs4887062	CHRNA5	cis	Heart Left Ventricle	GTEx
rs4887062	RP11-650L12.2	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78833600-78838400	Weak transcription	Spleen	Spleen
2	chr15:78833800-78838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:78833800-78838000	Weak transcription	Esophagus	oesophagus
4	chr15:78833800-78838000	Weak transcription	Gastric	stomach
5	chr15:78833800-78838400	Weak transcription	Pancreas	Pancrea
6	chr15:78834000-78838000	Weak transcription	Small Intestine	intestine
7	chr15:78834200-78841200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:78834200-78843400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:78834200-78843400	Strong transcription	Placenta	Placenta
10	chr15:78834200-78845000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:78834400-78843600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:78834400-78843600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:78834400-78843800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr15:78834400-78843800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr15:78834600-78843200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:78834600-78843600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:78834600-78843800	Strong transcription	Fetal Muscle Leg	muscle
18	chr15:78834800-78839600	Strong transcription	Lung	lung
19	chr15:78834800-78842400	Strong transcription	Osteobl	bone
20	chr15:78834800-78843200	Strong transcription	HUVEC	blood vessel
21	chr15:78834800-78843400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:78834800-78843600	Strong transcription	H9 Cell Line	embryonic stem cell
23	chr15:78834800-78843600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:78834800-78843600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:78834800-78843600	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr15:78834800-78843800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr15:78834800-78843800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:78834800-78843800	Strong transcription	Colon Smooth Muscle	Colon
29	chr15:78834800-78843800	Strong transcription	Stomach Smooth Muscle	stomach
30	chr15:78834800-78844200	Strong transcription	Fetal Thymus	thymus
31	chr15:78835000-78838400	Strong transcription	NHDF-Ad	bronchial
32	chr15:78835000-78839800	Strong transcription	NHEK	skin
33	chr15:78835000-78840200	Strong transcription	Fetal Kidney	kidney
34	chr15:78835000-78842200	Strong transcription	HMEC	breast
35	chr15:78835000-78842800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:78835000-78843600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr15:78835000-78843600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:78835000-78843600	Strong transcription	Duodenum Mucosa	Duodenum
39	chr15:78835000-78843600	Strong transcription	Fetal Intestine Large	intestine
40	chr15:78835000-78843600	Strong transcription	HSMM	muscle
41	chr15:78835000-78843800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr15:78835000-78843800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr15:78835000-78843800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:78835000-78843800	Strong transcription	Fetal Brain Female	brain
45	chr15:78835000-78844000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr15:78835000-78844000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:78835000-78844600	Strong transcription	Primary B cells from cord blood	blood
48	chr15:78835200-78838000	Weak transcription	Right Ventricle	heart
49	chr15:78835200-78839400	Weak transcription	Fetal Heart	heart
50	chr15:78835200-78843600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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