Variant report

Variant	rs12569084
Chromosome Location	chr1:166943352-166943353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1041238	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs10918600	1.00[GIH][hapmap]
rs10918603	1.00[GIH][hapmap]
rs10918607	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs10918608	0.82[ASN][1000 genomes]
rs11578336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11579987	0.95[GIH][hapmap]
rs11802666	0.84[ASN][1000 genomes]
rs11805946	0.85[ASN][1000 genomes]
rs12118335	0.81[ASN][1000 genomes]
rs12126991	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12131832	0.81[ASN][1000 genomes]
rs12133327	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12134016	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs12564877	0.82[ASN][1000 genomes]
rs2235184	0.95[GIH][hapmap]
rs2296837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2312487	0.83[ASN][1000 genomes]
rs2312675	0.80[CHB][hapmap]
rs3736988	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs41269702	0.97[ASN][1000 genomes]
rs56093705	0.81[ASN][1000 genomes]
rs61447801	0.85[ASN][1000 genomes]
rs61606407	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427047	0.95[GIH][hapmap]
rs6427053	0.88[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs6655947	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6660048	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6662130	0.85[ASN][1000 genomes]
rs6665341	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669886	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs6673622	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6673720	0.88[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap]
rs6681562	0.81[ASN][1000 genomes]
rs6681571	0.81[ASN][1000 genomes]
rs6682062	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6695162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6695609	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6696203	0.88[CHB][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs6697417	0.86[ASN][1000 genomes]
rs6699159	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs742048	0.95[GIH][hapmap]
rs7511933	0.85[ASN][1000 genomes]
rs7518155	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7528849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7533688	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7545806	1.00[GIH][hapmap]
rs7545911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7550698	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12569084	RGS4	cis	parietal	SCAN
rs12569084	TBX19	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166940800-166943400	Weak transcription	Thymus	Thymus
2	chr1:166941400-166943800	Enhancers	Fetal Heart	heart
3	chr1:166941600-166944000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:166941800-166944000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
5	chr1:166941800-166945400	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr1:166942200-166943400	Enhancers	Brain Anterior Caudate	brain
7	chr1:166942200-166943400	Active TSS	Brain Hippocampus Middle	brain
8	chr1:166942200-166943600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:166942200-166943800	Bivalent Enhancer	Fetal Thymus	thymus
10	chr1:166942200-166945800	Active TSS	Fetal Brain Female	brain
11	chr1:166942400-166943400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:166942400-166944000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
13	chr1:166942400-166944200	Weak transcription	Spleen	Spleen
14	chr1:166942600-166943600	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:166942600-166943800	Weak transcription	Pancreas	Pancrea
16	chr1:166943000-166943400	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:166943000-166943800	Enhancers	Fetal Brain Male	brain
18	chr1:166943000-166943800	Flanking Active TSS	HSMMtube	muscle
19	chr1:166943000-166944000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:166943000-166944000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
21	chr1:166943000-166944000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:166943000-166944000	Flanking Active TSS	Brain Cingulate Gyrus	brain
23	chr1:166943000-166944200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:166943000-166944400	Flanking Active TSS	Dnd41	blood
25	chr1:166943000-166944400	Flanking Active TSS	GM12878-XiMat	blood
26	chr1:166943200-166943400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
27	chr1:166943200-166943400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:166943200-166943400	Flanking Active TSS	HSMM	muscle
29	chr1:166943200-166943600	Bivalent Enhancer	Fetal Muscle Leg	muscle
30	chr1:166943200-166943600	Enhancers	Right Ventricle	heart
31	chr1:166943200-166943800	Active TSS	Brain Angular Gyrus	brain
32	chr1:166943200-166943800	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr1:166943200-166943800	Bivalent Enhancer	Rectal Smooth Muscle	rectum
34	chr1:166943200-166945400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
35	chr1:166943200-166945400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:166943200-166945600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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