Variant report

Variant	rs12903907
Chromosome Location	chr15:34321981-34321982
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	chr15:34320977..34323643-chr15:34328767..34331333,2	MCF-7	breast:
2	chr15:34308484..34310036-chr15:34321852..34323927,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11072868	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs11635479	0.98[EUR][1000 genomes]
rs11638109	0.97[EUR][1000 genomes]
rs12437606	0.91[ASN][1000 genomes]
rs12443077	0.87[ASN][1000 genomes]
rs12898898	1.00[EUR][1000 genomes]
rs12913747	0.95[EUR][1000 genomes]
rs12917116	0.85[ASN][1000 genomes]
rs1436922	1.00[JPT][hapmap]
rs2279423	0.87[ASN][1000 genomes]
rs2339352	0.95[CEU][hapmap];0.85[YRI][hapmap];0.97[EUR][1000 genomes]
rs2632073	0.91[ASN][1000 genomes]
rs2632077	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2632110	0.91[ASN][1000 genomes]
rs2684940	0.97[EUR][1000 genomes]
rs2705338	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs34474029	0.88[EUR][1000 genomes]
rs34773983	0.95[EUR][1000 genomes]
rs35531038	0.96[EUR][1000 genomes]
rs35804445	0.89[EUR][1000 genomes]
rs4477671	0.96[EUR][1000 genomes]
rs4779652	0.95[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs4779656	0.95[CEU][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs4780203	0.90[EUR][1000 genomes]
rs483279	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs486230	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs488762	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs489349	1.00[CHD][hapmap]
rs489945	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs514472	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs519152	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs519210	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs520032	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs520935	1.00[CHD][hapmap]
rs532720	0.81[CEU][hapmap]
rs536345	0.95[CEU][hapmap];0.94[EUR][1000 genomes]
rs541098	0.88[ASN][1000 genomes]
rs602302	0.94[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs618868	0.91[EUR][1000 genomes]
rs62014670	0.81[EUR][1000 genomes]
rs62014671	0.81[EUR][1000 genomes]
rs62014673	0.85[ASN][1000 genomes]
rs632591	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs639860	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs640291	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs646339	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs647721	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6495442	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs6495443	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs66530874	1.00[EUR][1000 genomes]
rs67739072	1.00[EUR][1000 genomes]
rs685516	1.00[CHD][hapmap]
rs71462883	0.95[EUR][1000 genomes]
rs71464844	0.81[EUR][1000 genomes]
rs7162140	0.98[EUR][1000 genomes]
rs7163545	1.00[CHD][hapmap]
rs7168640	0.83[EUR][1000 genomes]
rs7169003	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs7173183	0.98[EUR][1000 genomes]
rs7175823	0.95[CEU][hapmap];0.97[TSI][hapmap];1.00[EUR][1000 genomes]
rs7175933	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7178075	0.95[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs7178446	0.95[CEU][hapmap];0.95[EUR][1000 genomes]
rs72718678	1.00[EUR][1000 genomes]
rs72718682	1.00[EUR][1000 genomes]
rs8030094	0.95[CEU][hapmap];0.92[GIH][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs8039219	0.81[ASN][1000 genomes]
rs9672432	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456789	chr15:34034421-34426618	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv568920	chr15:34034421-34426618	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv471235	chr15:34035529-34421951	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv903985	chr15:34279319-34370487	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12903907	CHRM5	cis	parietal	SCAN
rs12903907	AVEN	Cis_1M	lymphoblastoid	RTeQTL
rs12903907	CHRM5	cis	cerebellum	SCAN
rs12903907	RYR3	cis	parietal	SCAN
rs12903907	NDNL2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34309400-34330000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr15:34309600-34330000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:34314200-34326400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:34316600-34329400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr15:34320200-34329800	Weak transcription	Hela-S3	cervix
6	chr15:34320400-34326400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:34320600-34327000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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