Variant report

Variant	rs10879433
Chromosome Location	chr12:72879805-72879806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:72879336..72881093-chr12:72890527..72893144,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10161472	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs10506655	0.87[TSI][hapmap]
rs10879422	1.00[CEU][hapmap]
rs10879429	0.86[MEX][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs10879430	0.86[EUR][1000 genomes]
rs10879431	0.86[EUR][1000 genomes]
rs10879432	1.00[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10879435	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10879438	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10879440	0.82[EUR][1000 genomes]
rs10879441	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs10879467	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs10879468	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs10879469	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs10879470	1.00[CEU][hapmap]
rs11179199	0.82[EUR][1000 genomes]
rs11179236	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11179242	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs11179285	1.00[CEU][hapmap]
rs11179291	1.00[CEU][hapmap]
rs12297047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12301567	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12322905	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12367387	1.00[CEU][hapmap]
rs12370001	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs12370471	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap]
rs12372580	0.87[EUR][1000 genomes]
rs1387977	1.00[CEU][hapmap]
rs1444602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17111240	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17111392	1.00[CEU][hapmap]
rs17111405	1.00[CEU][hapmap]
rs17111445	1.00[CEU][hapmap]
rs17111496	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs1821310	1.00[CEU][hapmap]
rs1821311	1.00[CEU][hapmap]
rs2217678	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs7139238	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs7308664	1.00[CEU][hapmap];1.00[GIH][hapmap]
rs9645830	0.87[TSI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv899258	chr12:72624088-72957899	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	nsv832453	chr12:72778058-72966827	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	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
10	nsv469466	chr12:72830441-72885554	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv559364	chr12:72830441-72885554	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs10879433	GAP43	cis	Temporal Cortex	GTEx
rs10879433	C9orf45	cis	Temporal Cortex	GTEx
rs10879433	GIMAP8	cis	Temporal Cortex	GTEx
rs10879433	CNTNAP1	cis	Temporal Cortex	GTEx
rs10879433	SIPA1	cis	Temporal Cortex	GTEx
rs10879433	ZNF280B	cis	Temporal Cortex	GTEx
rs10879433	HERC5	cis	Temporal Cortex	GTEx
rs10879433	DBC1	cis	Temporal Cortex	GTEx
rs10879433	ANKRD57	cis	Temporal Cortex	GTEx
rs10879433	TM9SF4	cis	Temporal Cortex	GTEx
rs10879433	ACVR1B	cis	Temporal Cortex	GTEx
rs10879433	RAPGEFL1	cis	Temporal Cortex	GTEx
rs10879433	C12orf75	cis	Temporal Cortex	GTEx
rs10879433	PODN	cis	Temporal Cortex	GTEx
rs10879433	COPG	cis	Temporal Cortex	GTEx
rs10879433	NEFL	cis	Temporal Cortex	GTEx
rs10879433	GSDMD	cis	Temporal Cortex	GTEx
rs10879433	FCHSD2	cis	Temporal Cortex	GTEx
rs10879433	SFRS14	cis	Temporal Cortex	GTEx
rs10879433	VIPR1	cis	Temporal Cortex	GTEx
rs10879433	ATP5I	cis	Temporal Cortex	GTEx
rs10879433	GNPDA1	cis	Temporal Cortex	GTEx
rs10879433	TMSL3	cis	Temporal Cortex	GTEx
rs10879433	RPS29	cis	Temporal Cortex	GTEx
rs10879433	ARL3	cis	Temporal Cortex	GTEx
rs10879433	RPL6	cis	Temporal Cortex	GTEx
rs10879433	RPS8	cis	Temporal Cortex	GTEx
rs10879433	SLC15A3	cis	Temporal Cortex	GTEx
rs10879433	LPHN1	cis	Temporal Cortex	GTEx
rs10879433	EEF1D	cis	Temporal Cortex	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:72878600-72880600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr12:72878600-72880600	Strong transcription	Fetal Intestine Large	intestine
3	chr12:72878800-72880400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr12:72878800-72880400	Strong transcription	Adipose Nuclei	Adipose
5	chr12:72878800-72880600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr12:72879200-72880800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:72879400-72880400	ZNF genes & repeats	Fetal Intestine Small	intestine
8	chr12:72879400-72880600	Strong transcription	Pancreas	Pancrea
9	chr12:72879600-72881400	Weak transcription	Ovary	ovary
10	chr12:72879800-72880200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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