Variant report

Variant	rs12899131
Chromosome Location	chr15:78726885-78726886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78589324..78591746-chr15:78726632..78728415,2	K562	blood:
2	chr15:78722314..78725378-chr15:78725474..78727729,3	MCF-7	breast:

Extended variants
information (count: 25 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10519198	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11072762	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11072765	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11639224	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12909921	0.95[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910090	0.96[CEU][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16969899	0.85[LWK][hapmap]
rs1847529	0.96[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292116	0.88[LWK][hapmap]
rs2568498	0.96[CEU][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs2568500	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2656058	0.93[EUR][1000 genomes]
rs2869030	0.90[JPT][hapmap]
rs2869046	0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3743079	0.88[LWK][hapmap]
rs3817092	0.88[LWK][hapmap]
rs4390557	0.89[EUR][1000 genomes]
rs4436747	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8041628	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs954144	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
3	nsv833063	chr15:78605215-78754945	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1627	chr15:78683761-78728604	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs12899131	IREB2	cis	parietal	SCAN
rs12899131	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs12899131	RP11-650L12.2	cis	lung	GTEx
rs12899131	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs12899131	CHRNA5	cis	cerebellum	SCAN
rs12899131	UBE2Q2	cis	cerebellum	SCAN
rs12899131	CHRNA5	cis	Muscle Skeletal	GTEx
rs12899131	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs12899131	CHRNA5	cis	parietal	SCAN
rs12899131	CHRNA5	cis	Heart Left Ventricle	GTEx
rs12899131	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs12899131	CHRNA5	cis	Nerve Tibial	GTEx
rs12899131	IREB2	cis	cerebellum	SCAN
rs12899131	RP11-650L12.2	cis	Nerve Tibial	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78698200-78729800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78720800-78728400	Weak transcription	K562	blood
3	chr15:78725000-78729400	Weak transcription	Liver	Liver
4	chr15:78726000-78727200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:78726200-78727200	Enhancers	Rectal Mucosa Donor 31	rectum
6	chr15:78726400-78729600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr15:78726600-78727000	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr15:78726600-78727800	Enhancers	HepG2	liver
9	chr15:78726800-78729000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:78726800-78729400	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr15:78726800-78729400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr15:78726800-78729600	Weak transcription	Duodenum Mucosa	Duodenum
13	chr15:78726800-78729600	Weak transcription	Monocytes-CD14+_RO01746	blood

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