Variant report

Variant	rs11165379
Chromosome Location	chr1:95788826-95788827
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10874912	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10874914	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11165366	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165367	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11165374	0.81[EUR][1000 genomes]
rs11165375	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12116466	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12118116	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12135605	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141215	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12142805	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12565207	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12752448	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1548278	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17589093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2182021	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2893323	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34009737	0.86[AMR][1000 genomes]
rs34988332	0.91[AMR][1000 genomes]
rs4129611	0.91[AMR][1000 genomes]
rs4359066	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4394708	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4408199	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4604740	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61771812	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66930640	0.91[AMR][1000 genomes]
rs72723875	0.93[AMR][1000 genomes]
rs912648	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs927703	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830648	chr1:95760162-95926264	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1006113	chr1:95768502-96139003	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv529002	chr1:95781217-95805002	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11165379	TMEM56	cis	cerebellum	SCAN
rs11165379	FAM69A	cis	parietal	SCAN
rs11165379	OR8B4	trans	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95786800-95789200	Enhancers	HUES64 Cell Line	embryonic stem cell
2	chr1:95786800-95789600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr1:95787000-95789400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:95787400-95789000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr1:95787400-95789000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:95787600-95789800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:95787800-95789000	Weak transcription	Brain Anterior Caudate	brain
8	chr1:95787800-95789200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:95787800-95789400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:95787800-95789600	Enhancers	Brain Substantia Nigra	brain
11	chr1:95787800-95790000	Enhancers	Brain Hippocampus Middle	brain
12	chr1:95788000-95790600	Weak transcription	Fetal Brain Female	brain
13	chr1:95788200-95789000	Enhancers	Brain Angular Gyrus	brain
14	chr1:95788400-95789600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:95788400-95791200	Enhancers	Brain Cingulate Gyrus	brain
16	chr1:95788600-95789200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr1:95788600-95789400	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:95788600-95790600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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