Variant report

Variant	rs7309958
Chromosome Location	chr12:48836889-48836890
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10747550	0.93[CEU][hapmap]
rs10783262	0.92[CEU][hapmap]
rs1895999	0.93[CEU][hapmap]
rs2252234	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468939	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2705125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2705131	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2705134	0.82[ASN][1000 genomes]
rs2731063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2731092	0.90[CHB][hapmap];0.81[YRI][hapmap]
rs2731096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2731099	0.81[CHB][hapmap];0.81[YRI][hapmap]
rs2731105	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2731106	0.82[JPT][hapmap];0.82[YRI][hapmap]
rs2732447	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2956465	0.82[ASN][1000 genomes]
rs2956466	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34478996	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34801828	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4369449	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs4492859	0.93[CEU][hapmap]
rs4635128	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7139348	0.90[CHB][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes]
rs71464905	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7956260	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427911	chr12:48670336-48979396	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv832402	chr12:48686761-48851020	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7309958	MGC35033	cis	multi-tissue	Pritchard
rs7309958	C12orf54	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48833800-48840400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr12:48834200-48840400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48834200-48840400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:48834600-48837800	Enhancers	Hela-S3	cervix
5	chr12:48835400-48838600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:48835800-48837200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:48836400-48839600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr12:48836600-48839600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:48836600-48839600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:48836800-48839800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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