Variant report

Variant	rs7306825
Chromosome Location	chr12:103771416-103771417
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10047640	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10778231	0.81[CEU][hapmap]
rs10778237	0.82[CEU][hapmap]
rs10860989	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10860990	0.87[CEU][hapmap]
rs11111537	0.82[ASW][hapmap];0.90[CEU][hapmap];0.81[GIH][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11111539	0.82[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11111540	0.82[CEU][hapmap]
rs12305336	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2374060	0.86[CEU][hapmap]
rs4764733	0.82[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6539069	0.86[CEU][hapmap]
rs6539070	0.85[CEU][hapmap]
rs7312908	0.89[CEU][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7316140	0.95[CEU][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7966251	0.81[EUR][1000 genomes]
rs7970531	0.87[CEU][hapmap]

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	nsv455703	chr12:103692799-103818049	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
2	nsv560037	chr12:103692799-103818049	Enhancers Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv899477	chr12:103747515-103817326	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv899478	chr12:103747515-103834275	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7306825	EID3	cis	cerebellum	SCAN
rs7306825	ACTR6	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:103707200-103786400	Weak transcription	Primary B cells from cord blood	blood
2	chr12:103763600-103786400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr12:103767800-103776600	Weak transcription	Thymus	Thymus
4	chr12:103771000-103773600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:103771200-103772000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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