Variant report

Variant	rs12674871
Chromosome Location	chr8:9979144-9979145
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10107485	0.80[CHB][hapmap];0.89[JPT][hapmap]
rs1160369	0.82[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11774411	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11783851	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11785434	0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs11785454	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12542030	0.82[CHB][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs12545469	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12545775	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12545788	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12547884	0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12549943	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12550244	0.82[CHB][hapmap]
rs12680389	0.86[CHB][hapmap]
rs13256357	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1466555	0.82[ASN][1000 genomes]
rs1484645	0.92[CEU][hapmap];0.83[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1564808	0.81[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs17151128	0.91[YRI][hapmap]
rs17151142	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17151175	0.83[YRI][hapmap]
rs17151190	0.83[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17151201	0.92[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17155393	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1984863	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2016221	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28653100	0.81[ASN][1000 genomes]
rs2898242	0.82[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4294187	0.82[CHB][hapmap]
rs4840463	0.81[JPT][hapmap]
rs4841279	0.86[CHB][hapmap]
rs4841283	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57105322	0.81[ASN][1000 genomes]
rs66602888	0.83[EUR][1000 genomes]
rs6985791	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7008407	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs7008695	0.80[ASN][1000 genomes]
rs7012601	0.86[ASN][1000 genomes]
rs7016690	0.86[ASN][1000 genomes]
rs72626643	0.87[EUR][1000 genomes]
rs7830843	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7843906	0.81[CHD][hapmap]
rs9329215	0.82[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9644681	0.90[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	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv610263	chr8:9941021-10090149	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1034343	chr8:9948342-10014155	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv831230	chr8:9953343-10139350	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1027280	chr8:9958259-10058984	Enhancers Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1021921	chr8:9958259-10212555	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv1850829	chr8:9958321-10045451	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12674871	FLJ10661	cis	cerebellum	SCAN
rs12674871	FAM167A	cis	parietal	SCAN
rs12674871	DLC1	cis	cerebellum	SCAN
rs12674871	LONRF1	cis	parietal	SCAN
rs12674871	C8orf48	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9970600-9995800	Weak transcription	Pancreas	Pancrea
2	chr8:9974400-9979600	Weak transcription	Esophagus	oesophagus
3	chr8:9975600-9987400	Weak transcription	Brain Germinal Matrix	brain
4	chr8:9977000-9988000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr8:9978200-9988000	Weak transcription	Fetal Brain Female	brain
6	chr8:9978600-9979800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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