Variant report

Variant	rs12760895
Chromosome Location	chr1:62764663-62764664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10493320	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207957	1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs12058486	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12063531	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12065844	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12078087	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12079207	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12082238	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.86[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12085325	0.95[ASN][1000 genomes]
rs12718429	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12724349	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12760226	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2296518	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2477872	0.94[ASN][1000 genomes]
rs2666487	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2666488	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2666503	0.80[MEX][hapmap]
rs2666508	0.82[GIH][hapmap];0.80[MEX][hapmap]
rs2765251	0.80[AMR][1000 genomes]
rs2765258	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2765261	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs2765263	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs34752481	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7520614	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[ASN][1000 genomes]
rs765691	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs765692	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs912894	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	nsv431712	chr1:62759369-62766001	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12760895	DAB1	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62754400-62773400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:62754800-62765200	Weak transcription	Fetal Heart	heart
3	chr1:62756200-62765000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:62756400-62764800	Weak transcription	HepG2	liver
5	chr1:62759800-62765400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:62759800-62770800	Enhancers	Fetal Muscle Leg	muscle
7	chr1:62761800-62765000	Weak transcription	Fetal Kidney	kidney
8	chr1:62761800-62767200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:62762000-62764800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr1:62762000-62765000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr1:62762000-62765400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:62762000-62765600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr1:62762000-62766000	Weak transcription	Brain Angular Gyrus	brain
14	chr1:62762000-62767000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:62762200-62765000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:62762200-62765000	Weak transcription	Fetal Thymus	thymus
17	chr1:62762200-62765000	Weak transcription	Left Ventricle	heart
18	chr1:62762200-62765000	Weak transcription	Right Atrium	heart
19	chr1:62762200-62765000	Weak transcription	HMEC	breast
20	chr1:62762200-62765000	Weak transcription	HSMM	muscle
21	chr1:62762200-62765200	Weak transcription	HSMMtube	muscle
22	chr1:62762200-62765400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:62762200-62765600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:62762200-62765600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:62762200-62767200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:62762200-62773200	Weak transcription	Fetal Lung	lung
27	chr1:62762400-62764800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:62762400-62765000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr1:62762400-62765000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:62762400-62765000	Weak transcription	Brain Substantia Nigra	brain
31	chr1:62762400-62765200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:62762400-62765200	Weak transcription	Adipose Nuclei	Adipose
33	chr1:62762400-62765200	Weak transcription	Brain Anterior Caudate	brain
34	chr1:62762400-62765200	Weak transcription	Brain Hippocampus Middle	brain
35	chr1:62762400-62765400	Weak transcription	Brain Germinal Matrix	brain
36	chr1:62762600-62765000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:62762600-62765600	Weak transcription	Brain Cingulate Gyrus	brain
38	chr1:62762800-62765000	Weak transcription	Fetal Muscle Trunk	muscle
39	chr1:62763200-62765000	Weak transcription	Fetal Stomach	stomach
40	chr1:62763200-62765200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:62763200-62765800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:62764400-62764800	Weak transcription	Pancreas	Pancrea
43	chr1:62764400-62764800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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