Variant report

Variant	rs4567478
Chromosome Location	chr11:120577423-120577424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:120576655..120578167-chr11:120777548..120780496,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11217978	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11217979	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11217980	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11217981	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11217983	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11217984	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11217987	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11217989	1.00[CEU][hapmap];0.86[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12270261	0.81[CEU][hapmap]
rs12270409	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12272864	0.81[CEU][hapmap]
rs12274300	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12276408	0.80[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12276440	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12278795	0.81[CEU][hapmap]
rs12280296	0.81[CEU][hapmap]
rs12281464	0.91[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12281614	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12291927	0.81[CEU][hapmap]
rs12293393	0.81[CEU][hapmap]
rs12294858	0.85[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12295113	0.81[CEU][hapmap]
rs12295200	0.81[CEU][hapmap]
rs17124211	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2846109	0.81[CEU][hapmap]
rs2852225	0.81[CEU][hapmap]
rs2852227	0.81[CEU][hapmap]
rs28781001	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61901379	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61901380	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61902685	0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs61902688	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7102869	0.81[CEU][hapmap]
rs7103021	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7103228	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs7103418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7119619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7944756	0.91[CEU][hapmap]
rs7946325	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9630199	0.90[CEU][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9630200	0.90[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][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	nsv1054407	chr11:120535570-120630114	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1053607	chr11:120540795-120802006	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	esv3693392	chr11:120549745-120628012	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4567478	TMEM136	cis	cerebellum	SCAN
rs4567478	C2CD2L	cis	parietal	SCAN
rs4567478	FXYD6	cis	parietal	SCAN
rs4567478	TAGLN	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120568000-120580600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr11:120570000-120581600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:120575200-120577800	Weak transcription	Ovary	ovary
4	chr11:120576200-120578000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr11:120577000-120578600	ZNF genes & repeats	Pancreas	Pancrea
6	chr11:120577200-120577800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:120577200-120578000	ZNF genes & repeats	Spleen	Spleen
8	chr11:120577400-120578800	Strong transcription	Fetal Lung	lung

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