Variant report

Variant	rs10879467
Chromosome Location	chr12:73011367-73011368
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10161472	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10784980	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10879432	1.00[CEU][hapmap]
rs10879433	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs10879435	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10879438	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10879440	0.90[EUR][1000 genomes]
rs10879441	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs10879468	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10879469	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10879470	1.00[CEU][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10879471	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11179236	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11179242	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11179251	0.96[EUR][1000 genomes]
rs11179252	1.00[EUR][1000 genomes]
rs11179265	1.00[EUR][1000 genomes]
rs11179278	0.96[EUR][1000 genomes]
rs11179283	1.00[EUR][1000 genomes]
rs11179285	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11179291	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11179301	1.00[EUR][1000 genomes]
rs11179306	0.83[TSI][hapmap];1.00[EUR][1000 genomes]
rs12297047	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs12301567	1.00[CEU][hapmap]
rs12322905	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs12370001	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes]
rs12370471	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs1387977	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1444602	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs17111240	0.86[EUR][1000 genomes]
rs17111392	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17111405	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17111445	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17111496	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1821310	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1821311	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2217678	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7139238	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7308664	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74105937	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422452	chr12:72485933-73175581	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv899257	chr12:72569746-73145896	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv1044083	chr12:72647640-73275526	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv469465	chr12:72655925-73259114	Weak transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv559363	chr12:72655925-73259114	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv868884	chr12:72664763-73241518	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv817280	chr12:72820558-73508605	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv899259	chr12:72885554-73011367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv832454	chr12:72940798-73081180	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv1805187	chr12:72949787-73013475	Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1054725	chr12:72990553-73062598	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	esv2758314	chr12:72990707-73251109	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	esv2759908	chr12:72990707-73251109	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv868885	chr12:72998553-73587081	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs10879467	ANKRD57	cis	Temporal Cortex	GTEx
rs10879467	SERBP1	cis	Temporal Cortex	GTEx
rs10879467	GAP43	cis	Temporal Cortex	GTEx
rs10879467	RAPGEFL1	cis	Temporal Cortex	GTEx
rs10879467	ATP5I	cis	Temporal Cortex	GTEx
rs10879467	NEFL	cis	Temporal Cortex	GTEx
rs10879467	CNTNAP1	cis	Temporal Cortex	GTEx
rs10879467	HERC5	cis	Temporal Cortex	GTEx
rs10879467	USP11	cis	Temporal Cortex	GTEx
rs10879467	TMSL3	cis	Temporal Cortex	GTEx
rs10879467	PPFIA2	cis	Temporal Cortex	GTEx
rs10879467	RPL6	cis	Temporal Cortex	GTEx
rs10879467	SFRS14	cis	Temporal Cortex	GTEx
rs10879467	FCHSD2	cis	Temporal Cortex	GTEx
rs10879467	TM9SF4	cis	Temporal Cortex	GTEx
rs10879467	RPS29	cis	Temporal Cortex	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:73005000-73051600	Weak transcription	Fetal Intestine Large	intestine
2	chr12:73005200-73038000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:73005200-73053200	Weak transcription	Ovary	ovary

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