Variant report

Variant	rs12889741
Chromosome Location	chr14:70886032-70886033
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	YY1	chr14:70885991-70886591	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:70884634..70887118-chr14:70904872..70907534,2	MCF-7	breast:

Variant related genes	Relation type
SYNJ2BP-COX16	TF binding region
SYNJ2BP	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10133282	0.87[ASN][1000 genomes]
rs10139500	0.93[ASN][1000 genomes]
rs10142102	0.83[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10144818	0.90[ASN][1000 genomes]
rs10148586	0.83[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs10150707	0.88[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1044527	0.85[JPT][hapmap]
rs11158861	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11623974	0.85[JPT][hapmap]
rs11626325	0.86[AFR][1000 genomes]
rs11844845	0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs12588623	0.85[ASN][1000 genomes]
rs12589762	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887715	0.86[AFR][1000 genomes]
rs12894199	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1959485	1.00[CHB][hapmap];0.90[GIH][hapmap]
rs2332384	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2877657	0.84[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs3759774	0.85[JPT][hapmap]
rs4541006	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4899354	1.00[CHB][hapmap]
rs4902815	1.00[ASW][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[TSI][hapmap];0.95[ASN][1000 genomes]
rs55728800	0.85[ASN][1000 genomes]
rs56977342	0.81[ASN][1000 genomes]
rs57495576	0.81[ASN][1000 genomes]
rs58186506	0.92[ASN][1000 genomes]
rs59788049	0.97[ASN][1000 genomes]
rs61979082	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66886776	0.99[ASN][1000 genomes]
rs7141636	0.90[ASN][1000 genomes]
rs7144478	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7148445	0.81[ASN][1000 genomes]
rs8014179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs8015005	0.90[JPT][hapmap]
rs9323536	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs9652366	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv902075	chr14:70612618-70919016	Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12889741	MED6	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70884000-70889000	Weak transcription	Fetal Muscle Leg	muscle
2	chr14:70884400-70886400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr14:70884400-70888600	Weak transcription	HSMM	muscle
4	chr14:70884800-70886200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr14:70885800-70887600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr14:70886000-70886200	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr14:70886000-70886800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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