Variant report

Variant	rs2248978
Chromosome Location	chr12:105328335-105328336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10507185	0.88[CEU][hapmap]
rs10778354	0.88[CEU][hapmap]
rs10778357	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10861281	0.86[CHD][hapmap]
rs10861282	0.88[CEU][hapmap]
rs10861291	0.88[CEU][hapmap]
rs10861292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11112234	0.88[CEU][hapmap]
rs12230601	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1466718	0.88[CHD][hapmap]
rs17829927	0.88[CEU][hapmap]
rs2220813	0.86[CHD][hapmap]
rs2249454	0.81[GIH][hapmap]
rs2252839	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2468097	0.86[CHD][hapmap]
rs2468396	0.81[EUR][1000 genomes]
rs2468397	0.88[CEU][hapmap]
rs2468398	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2731031	0.86[CHD][hapmap]
rs3890816	0.88[CEU][hapmap];0.90[CHB][hapmap]
rs4409923	0.88[CEU][hapmap];0.87[CHB][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4644704	0.88[CEU][hapmap]
rs4964116	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[GIH][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4964305	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7133934	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7959777	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs7965314	0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7973707	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2248978	C12orf42	cis	cerebellum	SCAN
rs2248978	ASCL1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105290800-105331600	Weak transcription	Gastric	stomach
2	chr12:105320200-105332200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:105323600-105338000	Weak transcription	Pancreas	Pancrea
4	chr12:105324800-105332200	Weak transcription	NHDF-Ad	bronchial
5	chr12:105325000-105332200	Weak transcription	Aorta	Aorta
6	chr12:105325000-105332400	Weak transcription	Osteobl	bone
7	chr12:105325600-105332400	Weak transcription	Liver	Liver
8	chr12:105325800-105328400	Enhancers	GM12878-XiMat	blood

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