Variant report

Variant	rs6427047
Chromosome Location	chr1:166914258-166914259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10800276	0.94[CEU][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs10918599	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10918600	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10918603	0.88[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10918607	0.82[CEU][hapmap];0.80[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap]
rs11576904	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11578336	0.80[CHD][hapmap];0.95[GIH][hapmap]
rs11579987	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11588176	0.98[ASN][1000 genomes]
rs12562794	0.83[CEU][hapmap]
rs12569084	0.95[GIH][hapmap]
rs1476347	0.83[CEU][hapmap]
rs2038020	0.90[ASN][1000 genomes]
rs2038022	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2072742	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2075946	0.82[CEU][hapmap]
rs2142615	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2235184	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2280995	0.88[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs2294220	0.97[ASN][1000 genomes]
rs2312675	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3820387	0.83[CEU][hapmap]
rs4657613	0.94[CEU][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs61815130	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61815132	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6427048	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6660048	0.82[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap]
rs6677644	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6695162	0.95[GIH][hapmap]
rs6695609	0.82[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes]
rs6699159	0.95[GIH][hapmap]
rs742048	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7518155	0.95[GIH][hapmap]
rs7520897	0.93[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7528849	0.95[GIH][hapmap]
rs7533688	0.95[GIH][hapmap]
rs7545806	0.88[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7545911	0.95[GIH][hapmap]

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	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
2	esv3332845	chr1:166913225-166914648	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6427047	RGS4	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166891000-166916400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:166905800-166915200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:166912800-166915400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:166912800-166915400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr1:166912800-166915400	Enhancers	Dnd41	blood
6	chr1:166912800-166916000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr1:166913000-166914400	Enhancers	Osteobl	bone
8	chr1:166913000-166916200	Enhancers	Brain Germinal Matrix	brain
9	chr1:166913000-166916400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:166913000-166916400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:166913000-166922200	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr1:166913400-166914400	Enhancers	Muscle Satellite Cultured Cells	--
13	chr1:166913400-166914400	Enhancers	Brain Cingulate Gyrus	brain
14	chr1:166913400-166914600	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr1:166913400-166915200	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:166913400-166915200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr1:166913400-166915200	Enhancers	Fetal Thymus	thymus
18	chr1:166913400-166915400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:166913400-166922000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:166913600-166914400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr1:166913600-166914400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr1:166913600-166914400	Enhancers	GM12878-XiMat	blood
23	chr1:166913600-166914600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr1:166913600-166914600	Enhancers	HMEC	breast
25	chr1:166913600-166914800	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr1:166913600-166915200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr1:166913800-166914400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:166913800-166914400	Enhancers	Fetal Brain Male	brain
29	chr1:166913800-166914400	Weak transcription	Fetal Heart	heart
30	chr1:166913800-166914600	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr1:166913800-166914600	Enhancers	Thymus	Thymus
32	chr1:166913800-166916400	Enhancers	Brain Angular Gyrus	brain
33	chr1:166914000-166914400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
34	chr1:166914000-166914400	Bivalent Enhancer	NHEK	skin
35	chr1:166914000-166915000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:166914000-166915800	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr1:166914000-166916000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr1:166914000-166916400	Enhancers	Brain Anterior Caudate	brain
39	chr1:166914000-166916400	Enhancers	Brain Hippocampus Middle	brain
40	chr1:166914000-166916400	Enhancers	Brain Substantia Nigra	brain
41	chr1:166914000-166923000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:166914200-166914400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:166914200-166915000	Weak transcription	Fetal Brain Female	brain
44	chr1:166914200-166915000	Enhancers	HSMMtube	muscle
45	chr1:166914200-166915200	Enhancers	HSMM	muscle
46	chr1:166914200-166916200	Bivalent Enhancer	NH-A	brain
47	chr1:166914200-166916400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:166914200-166916600	Weak transcription	Esophagus	oesophagus
49	chr1:166914200-166916600	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links