Variant report

Variant	rs6488910
Chromosome Location	chr12:124393697-124393698
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10773046	0.84[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs10773047	0.84[ASN][1000 genomes]
rs10846562	0.90[JPT][hapmap]
rs10846564	1.00[JPT][hapmap]
rs10846567	1.00[JPT][hapmap]
rs10846570	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs10846571	0.84[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10846572	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10846573	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10846574	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs10846575	0.92[ASN][1000 genomes]
rs10846576	0.97[ASN][1000 genomes]
rs10846580	0.83[YRI][hapmap]
rs11057381	1.00[JPT][hapmap]
rs11057383	1.00[JPT][hapmap]
rs11057388	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11057389	0.85[ASN][1000 genomes]
rs11057390	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11057391	0.82[ASN][1000 genomes]
rs12306328	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12307524	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12309481	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1317312	0.95[JPT][hapmap]
rs1317386	0.84[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1882489	1.00[JPT][hapmap]
rs1922258	1.00[JPT][hapmap]
rs2341569	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2341779	1.00[JPT][hapmap]
rs28435362	0.97[ASN][1000 genomes]
rs28528904	0.97[ASN][1000 genomes]
rs28654550	0.97[ASN][1000 genomes]
rs34587940	0.97[ASN][1000 genomes]
rs4390427	0.84[ASN][1000 genomes]
rs57078519	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57316347	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58411567	0.97[ASN][1000 genomes]
rs61587964	0.97[ASN][1000 genomes]
rs6488907	0.95[JPT][hapmap]
rs6488913	0.91[YRI][hapmap]
rs7296123	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7297429	0.81[ASN][1000 genomes]
rs7303634	0.86[ASN][1000 genomes]
rs7313897	1.00[JPT][hapmap]
rs7314278	0.81[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7959519	1.00[JPT][hapmap]
rs7961449	1.00[YRI][hapmap]
rs7964324	0.96[ASN][1000 genomes]
rs7970597	0.97[ASN][1000 genomes]
rs7976319	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7977078	0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7977713	0.90[JPT][hapmap]
rs7978781	0.97[ASN][1000 genomes]
rs9669530	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498024	chr12:123994372-124459856	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv1811815	chr12:124374716-124424636	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	esv1832870	chr12:124374716-124424636	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv522321	chr12:124383950-124424636	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv560499	chr12:124389150-124396816	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv560500	chr12:124393697-124396754	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv560501	chr12:124393697-124396878	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6488910	LRRC43	cis	cerebellum	SCAN
rs6488910	CCDC92	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:124384000-124408400	Weak transcription	Fetal Brain Female	brain
2	chr12:124386000-124395800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr12:124386200-124394000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:124390200-124397600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:124390800-124394400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:124391600-124394000	Enhancers	Placenta	Placenta
7	chr12:124391600-124395000	Enhancers	Fetal Muscle Leg	muscle
8	chr12:124391800-124393800	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr12:124392000-124393800	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr12:124392000-124393800	Enhancers	Brain Substantia Nigra	brain
11	chr12:124392000-124394200	Enhancers	Brain Cingulate Gyrus	brain
12	chr12:124392200-124394000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
13	chr12:124392200-124394400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
14	chr12:124392400-124393800	Weak transcription	Brain Germinal Matrix	brain
15	chr12:124392600-124393800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:124392600-124393800	Weak transcription	Brain Anterior Caudate	brain
17	chr12:124392600-124393800	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:124393000-124397200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr12:124393200-124394000	Weak transcription	Brain Angular Gyrus	brain
20	chr12:124393200-124398800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr12:124393400-124396800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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