Variant report

Variant	rs10918600
Chromosome Location	chr1:166919342-166919343
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10800276	0.88[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs10918599	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10918603	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10918607	0.88[CEU][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs11576904	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11578336	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs11579987	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11588176	0.97[ASN][1000 genomes]
rs12562794	0.80[TSI][hapmap]
rs12569084	1.00[GIH][hapmap]
rs2038020	0.87[ASN][1000 genomes]
rs2038022	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2072742	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2142615	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]
rs2235184	0.94[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280995	0.82[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs2294220	0.94[ASN][1000 genomes]
rs2312675	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657613	0.88[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs61815130	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61815132	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6427047	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]
rs6427048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6660048	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs6669886	0.81[CHB][hapmap]
rs6677644	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6695162	1.00[GIH][hapmap]
rs6695609	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes]
rs6699159	1.00[GIH][hapmap]
rs742048	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7518155	1.00[GIH][hapmap]
rs7520897	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs7528849	1.00[GIH][hapmap]
rs7533688	1.00[GIH][hapmap]
rs7545806	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7545911	1.00[GIH][hapmap]

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
rs10918600	RGS4	cis	parietal	SCAN
rs10918600	FAM78B	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166913000-166922200	Enhancers	Cortex derived primary cultured neurospheres	brain
2	chr1:166913400-166922000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:166914000-166923000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:166915400-166923800	Weak transcription	Dnd41	blood
5	chr1:166917000-166922400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:166917200-166922600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:166917400-166919600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr1:166917400-166919800	Enhancers	Brain Angular Gyrus	brain
9	chr1:166917400-166919800	Enhancers	Brain Substantia Nigra	brain
10	chr1:166917400-166920000	Enhancers	Brain Cingulate Gyrus	brain
11	chr1:166917400-166920400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:166917400-166922800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:166917600-166919400	Enhancers	Brain Hippocampus Middle	brain
14	chr1:166917600-166919600	Enhancers	Brain Anterior Caudate	brain
15	chr1:166917600-166920400	Weak transcription	Fetal Heart	heart
16	chr1:166917600-166921200	Weak transcription	HSMM	muscle
17	chr1:166917600-166921400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:166917800-166919600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr1:166918400-166920200	Enhancers	Fetal Brain Female	brain
20	chr1:166918400-166921600	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr1:166918400-166921800	Enhancers	Brain Germinal Matrix	brain
22	chr1:166918400-166922600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:166918800-166919400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:166918800-166920600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr1:166918800-166921600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr1:166918800-166922000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:166918800-166922400	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr1:166919000-166919400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr1:166919000-166920400	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr1:166919000-166920600	Enhancers	Fetal Brain Male	brain
31	chr1:166919000-166921000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr1:166919000-166921000	Enhancers	Stomach Smooth Muscle	stomach
33	chr1:166919000-166922800	Enhancers	Colon Smooth Muscle	Colon
34	chr1:166919200-166919600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
35	chr1:166919200-166919800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr1:166919200-166920000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:166919200-166920600	Weak transcription	HSMMtube	muscle

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