Variant report

Variant	rs12212582
Chromosome Location	chr6:118626480-118626481
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11758375	0.82[CHB][hapmap]
rs11758402	0.82[ASN][1000 genomes]
rs11968293	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs1572226	0.88[CHB][hapmap];0.81[MEX][hapmap];0.87[ASN][1000 genomes]
rs1690662	0.92[ASN][1000 genomes]
rs176014	0.83[YRI][hapmap]
rs1874081	0.85[ASN][1000 genomes]
rs188181	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs190756	0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs1923282	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs281861	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs281866	0.83[YRI][hapmap]
rs281867	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[YRI][hapmap];0.80[ASN][1000 genomes]
rs281868	0.94[CHB][hapmap];0.87[CHD][hapmap]
rs281872	0.83[YRI][hapmap]
rs283040	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs283042	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs283044	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs283045	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs283046	1.00[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap]
rs283047	0.85[ASN][1000 genomes]
rs283048	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs283049	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs283050	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs283051	0.85[ASN][1000 genomes]
rs283057	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs283061	0.85[ASN][1000 genomes]
rs283062	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs283066	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs283067	0.85[ASN][1000 genomes]
rs283077	0.94[CHB][hapmap]
rs283081	0.94[CHB][hapmap];0.87[CHD][hapmap];0.84[YRI][hapmap]
rs283082	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[YRI][hapmap]
rs283083	0.83[YRI][hapmap]
rs283084	0.94[CHB][hapmap]
rs283085	0.94[CHB][hapmap]
rs283086	0.94[CHB][hapmap]
rs283088	0.94[CHB][hapmap]
rs283091	0.94[CHB][hapmap];0.87[CHD][hapmap];0.81[YRI][hapmap]
rs369383	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs372237	1.00[CHB][hapmap];0.86[CHD][hapmap];0.84[YRI][hapmap]
rs376875	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs387266	0.82[ASN][1000 genomes]
rs387945	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[ASN][1000 genomes]
rs397445	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs399844	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs413876	0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs414091	0.95[YRI][hapmap];0.92[ASN][1000 genomes]
rs419592	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs422268	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs422833	0.94[CHB][hapmap];0.84[YRI][hapmap]
rs427027	0.82[YRI][hapmap]
rs431115	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs445099	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs445566	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.89[MKK][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs447193	0.94[CHB][hapmap]
rs450093	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4946333	0.94[CHB][hapmap];0.87[CHD][hapmap]
rs4946336	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6912208	0.88[CHB][hapmap]
rs6927800	0.82[CHB][hapmap]
rs731695	0.82[CHB][hapmap]
rs7452622	0.81[CHB][hapmap]
rs7749263	0.82[CHB][hapmap]
rs89107	0.94[CHB][hapmap]
rs927348	0.82[CHB][hapmap]
rs9401060	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs9489327	0.82[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530526	chr6:118027339-118718476	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv532051	chr6:118551027-119044197	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1020463	chr6:118593028-119146363	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12212582	C6orf204	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:118618600-118626800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr6:118621200-118627800	Weak transcription	Fetal Stomach	stomach
3	chr6:118621600-118627200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:118622400-118627000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:118625000-118631600	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr6:118625800-118627000	Weak transcription	Brain Germinal Matrix	brain
7	chr6:118626000-118627000	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:118626200-118627200	Weak transcription	Fetal Heart	heart
9	chr6:118626400-118626800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr6:118626400-118628600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr6:118626400-118629400	Enhancers	Aorta	Aorta

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