Variant report

Variant	rs10889387
Chromosome Location	chr1:63340845-63340846
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 110 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs10159426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10493327	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10736399	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10789129	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10889383	0.93[ASW][hapmap];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];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10889384	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10889385	0.85[ASN][1000 genomes]
rs10889386	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11208032	1.00[JPT][hapmap]
rs11208035	0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11208037	0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11208038	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11208040	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11208043	0.84[ASN][1000 genomes]
rs11208045	0.83[ASN][1000 genomes]
rs11208046	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11208047	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11208049	0.91[ASN][1000 genomes]
rs11208050	0.89[ASN][1000 genomes]
rs11208051	0.91[ASN][1000 genomes]
rs11208052	0.93[ASN][1000 genomes]
rs11208056	0.88[ASN][1000 genomes]
rs11579518	0.80[ASN][1000 genomes]
rs11580642	0.89[ASN][1000 genomes]
rs11584363	0.89[ASN][1000 genomes]
rs11587081	0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11803404	0.90[ASN][1000 genomes]
rs11804568	0.88[ASN][1000 genomes]
rs12128286	0.90[ASN][1000 genomes]
rs12134455	0.82[ASN][1000 genomes]
rs12567999	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12725996	0.93[ASN][1000 genomes]
rs12728111	0.89[ASN][1000 genomes]
rs12742537	0.89[ASN][1000 genomes]
rs12743698	0.85[ASN][1000 genomes]
rs12748640	0.85[ASN][1000 genomes]
rs12749904	0.93[ASN][1000 genomes]
rs12752360	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12756081	0.93[ASN][1000 genomes]
rs1333730	0.91[ASN][1000 genomes]
rs1333733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1333734	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1333736	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1360677	1.00[CEU][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1360678	0.87[ASN][1000 genomes]
rs1413242	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1537496	0.93[ASN][1000 genomes]
rs17097064	0.90[ASN][1000 genomes]
rs1931079	0.88[ASN][1000 genomes]
rs1981067	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2050248	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2366820	0.84[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2366821	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2366822	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2803238	0.80[CEU][hapmap];0.83[CHB][hapmap];0.87[GIH][hapmap]
rs2886770	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2886771	0.83[ASN][1000 genomes]
rs3211074	0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs3737892	0.85[ASN][1000 genomes]
rs3737893	0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4448545	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6587990	0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6587991	0.82[ASN][1000 genomes]
rs6587992	0.85[ASN][1000 genomes]
rs6587993	0.85[ASN][1000 genomes]
rs6587994	0.85[ASN][1000 genomes]
rs6587996	0.90[ASN][1000 genomes]
rs6587997	0.93[ASN][1000 genomes]
rs6587998	0.93[ASN][1000 genomes]
rs6656119	0.90[ASN][1000 genomes]
rs6657552	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660873	0.80[ASN][1000 genomes]
rs6663165	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6664673	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6665455	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6670072	0.88[ASN][1000 genomes]
rs6670694	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6676637	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6676821	0.88[ASN][1000 genomes]
rs6677051	0.85[ASN][1000 genomes]
rs6679582	0.96[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];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6683423	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6683732	0.87[ASN][1000 genomes]
rs6683832	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6685784	0.93[ASN][1000 genomes]
rs6686232	0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6687943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6693530	0.93[ASN][1000 genomes]
rs6695607	0.83[ASN][1000 genomes]
rs6699457	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7414021	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7512374	0.83[ASN][1000 genomes]
rs7512529	0.83[ASN][1000 genomes]
rs7515960	0.93[ASN][1000 genomes]
rs7519205	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7521483	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7522726	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7524508	0.83[ASN][1000 genomes]
rs7526246	0.89[ASN][1000 genomes]
rs7527423	0.90[ASN][1000 genomes]
rs7527905	0.85[ASN][1000 genomes]
rs7531329	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7535496	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7540030	1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7540205	0.87[ASN][1000 genomes]
rs7543380	0.85[EUR][1000 genomes]
rs7553110	0.89[ASN][1000 genomes]
rs7555606	0.89[ASN][1000 genomes]
rs998096	0.90[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	nsv830015	chr1:63261143-63455296	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10889387	ATG4C	cis	cerebellum	SCAN
rs10889387	ATG4C	cis	Thyroid	GTEx
rs10889387	ATG4C	cis	parietal	SCAN
rs10889387	ATG4C///CTR9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63298400-63345800	Weak transcription	Left Ventricle	heart
2	chr1:63336200-63341200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr1:63340000-63342400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:63340200-63341000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:63340400-63343200	Enhancers	Brain Hippocampus Middle	brain
6	chr1:63340600-63341200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:63340600-63341800	Enhancers	Brain Cingulate Gyrus	brain
8	chr1:63340600-63342400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:63340600-63342600	Enhancers	Brain Substantia Nigra	brain
10	chr1:63340600-63343200	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr1:63340800-63341800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:63340800-63342400	Enhancers	Brain Germinal Matrix	brain

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