Variant report

Variant	rs12209727
Chromosome Location	chr6:45353100-45353101
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:45344406..45349479-chr6:45352255..45358580,11	MCF-7	breast:
2	chr6:45344260..45347672-chr6:45348203..45354625,7	MCF-7	breast:
3	chr6:45352135..45354442-chr6:45361892..45364565,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196284	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10456552	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1080415	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10807318	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10948222	0.89[CHD][hapmap]
rs10948229	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10948231	0.89[ASN][1000 genomes]
rs12194311	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12208924	0.82[ASW][hapmap];0.86[CHD][hapmap];0.81[LWK][hapmap];0.80[MKK][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12524323	0.82[AMR][1000 genomes]
rs12525950	0.89[ASN][1000 genomes]
rs12529946	0.86[CHD][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs1285013	0.80[YRI][hapmap]
rs1285019	0.85[CHD][hapmap];0.81[MKK][hapmap];0.87[TSI][hapmap]
rs1321081	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16873345	0.81[CHD][hapmap]
rs17288278	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17288334	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1852986	0.96[CEU][hapmap];0.89[GIH][hapmap];0.81[LWK][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2396425	0.89[CHD][hapmap]
rs2396502	0.98[ASN][1000 genomes]
rs2396504	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35565233	0.82[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4072928	0.89[CHD][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4510673	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs62400336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458425	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs6458427	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs6901786	0.89[CHD][hapmap];0.81[LWK][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap]
rs6919873	0.81[ASW][hapmap]
rs6928753	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6932804	0.87[AMR][1000 genomes]
rs6933449	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6938177	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs717987	0.82[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7738526	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7757282	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7760342	0.88[CEU][hapmap]
rs7767025	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7769231	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9296455	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9296458	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9369558	0.89[CHD][hapmap]
rs9381373	0.96[CEU][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs9395088	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9463076	0.91[ASW][hapmap];0.88[CEU][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs9463081	0.89[CHD][hapmap]
rs9472451	0.89[CHD][hapmap];0.89[TSI][hapmap]
rs9472453	0.82[CHD][hapmap]
rs988147	0.81[ASW][hapmap];0.89[CHD][hapmap];0.89[TSI][hapmap]

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	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12209727	SUPT3H	cis	cerebellum	SCAN
rs12209727	SUPT3H	cis	parietal	SCAN
rs12209727	C6orf226	cis	cerebellum	SCAN
rs12209727	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL
rs12209727	CD2AP	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45347000-45355000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr6:45347200-45354200	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr6:45350600-45354400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:45350800-45354200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:45352800-45355000	Weak transcription	Placenta	Placenta

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