Variant report

Variant	rs12493778
Chromosome Location	chr3:155128631-155128632
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	chr3:155108548..155110604-chr3:155127196..155130080,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11706749	0.85[EUR][1000 genomes]
rs11709568	0.84[CHD][hapmap]
rs11713552	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11715278	1.00[JPT][hapmap]
rs11928089	0.86[JPT][hapmap]
rs12487150	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12496803	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12631218	0.88[CHD][hapmap]
rs12696031	0.88[CHD][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap]
rs13066178	0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13081656	0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13083852	0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs13100169	0.88[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs2351	0.86[CHD][hapmap]
rs2352	0.86[CHD][hapmap]
rs35424673	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4345113	0.85[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4630984	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap]
rs4679744	0.80[AMR][1000 genomes]
rs4679745	0.88[CHD][hapmap]
rs4680171	0.86[EUR][1000 genomes]
rs4680172	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs4680173	0.89[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.94[JPT][hapmap];0.84[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4680174	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680175	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680176	0.92[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4680177	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680185	0.86[CHD][hapmap]
rs6440985	0.93[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440993	0.83[CHD][hapmap]
rs6440994	0.81[CHD][hapmap]
rs6440995	0.81[CHD][hapmap]
rs6762452	0.90[EUR][1000 genomes]
rs6794214	0.85[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs6802079	0.88[CHD][hapmap]
rs6807784	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6807961	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7612603	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7615026	0.88[CHD][hapmap];0.88[JPT][hapmap]
rs7618495	0.84[CHD][hapmap]
rs7619730	0.91[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7627097	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9823946	0.85[JPT][hapmap]
rs9829532	0.84[CHD][hapmap]
rs9841365	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9848852	0.86[CHD][hapmap]
rs9869956	0.91[CHD][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	nsv999994	chr3:154579254-155175303	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv532664	chr3:154588346-155162615	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv1000753	chr3:154848433-155207022	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv536773	chr3:154848433-155207022	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12493778	KCNAB1	cis	cerebellum	SCAN
rs12493778	PLCH1	cis	parietal	SCAN
rs12493778	SLC33A1	cis	cerebellum	SCAN
rs12493778	GFM1	cis	cerebellum	SCAN
rs12493778	KCNAB1	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155125800-155134200	Weak transcription	Osteobl	bone
2	chr3:155127800-155128800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:155128200-155128800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:155128200-155130200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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