Variant report

Variant	rs10516959
Chromosome Location	chr4:96088849-96088850
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11724291	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11936736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11945547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1434540	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1434542	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1434543	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17023055	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023071	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023083	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17023105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17023119	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1836262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1865380	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2082656	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34585936	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3755881	0.89[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.85[MKK][hapmap]
rs3796438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796441	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3796447	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59204183	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59357293	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60968970	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6532533	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6826477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73839218	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7441644	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7662630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7674881	1.00[ASN][1000 genomes]
rs7682667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7691978	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv492312	chr4:95823124-96128327	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv830011	chr4:95947560-96103934	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv594907	chr4:95975470-96170439	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10516959	ABI1	trans	brain	seeQTL
rs10516959	APOBEC3C	trans	brain	seeQTL
rs10516959	SLC16A1	trans	brain	seeQTL
rs10516959	CCDC82	trans	brain	seeQTL
rs10516959	RNF11	trans	brain	seeQTL
rs10516959	NIPSNAP3A	trans	brain	seeQTL
rs10516959	SIPA1L3	trans	brain	seeQTL
rs10516959	NACA2	trans	brain	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:96059800-96100400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr4:96079400-96089000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr4:96080400-96098600	Weak transcription	Fetal Kidney	kidney
4	chr4:96081200-96091000	Weak transcription	Fetal Thymus	thymus
5	chr4:96084400-96090200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr4:96084600-96090200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr4:96084600-96111800	Weak transcription	Fetal Muscle Leg	muscle
8	chr4:96084800-96090800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr4:96084800-96099800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:96085200-96090200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr4:96087400-96089200	Enhancers	Fetal Lung	lung
12	chr4:96087400-96089400	Enhancers	Brain Cingulate Gyrus	brain
13	chr4:96087400-96089400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr4:96087400-96089800	Enhancers	Brain Hippocampus Middle	brain
15	chr4:96087600-96107000	Weak transcription	A549	lung
16	chr4:96087800-96089600	Weak transcription	Brain Anterior Caudate	brain
17	chr4:96087800-96090200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:96088000-96091800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr4:96088200-96089000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr4:96088200-96089200	Enhancers	Brain Angular Gyrus	brain
21	chr4:96088200-96091400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:96088200-96092000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr4:96088600-96090600	Strong transcription	Fetal Stomach	stomach
24	chr4:96088600-96091600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:96088800-96089000	Flanking Active TSS	Brain Substantia Nigra	brain
26	chr4:96088800-96089200	Strong transcription	Aorta	Aorta
27	chr4:96088800-96089200	Enhancers	Ovary	ovary
28	chr4:96088800-96091200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links