Variant report

Variant	rs6440985
Chromosome Location	chr3:155145352-155145353
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:155140732..155143652-chr3:155144981..155146803,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11706749	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11709568	0.86[CHD][hapmap]
rs11713552	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11715278	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11928089	0.86[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs12487150	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12493778	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]
rs12496803	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12631218	0.90[CHD][hapmap]
rs12696031	0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs13066178	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13081656	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13083852	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs13100169	0.86[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.83[ASN][1000 genomes]
rs2351	0.88[CHD][hapmap]
rs2352	0.88[CHD][hapmap]
rs35424673	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4345113	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.82[JPT][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4524323	0.81[ASN][1000 genomes]
rs4630984	0.88[CEU][hapmap];0.95[CHB][hapmap];0.92[JPT][hapmap]
rs4679744	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4679745	0.91[CHD][hapmap]
rs4680171	0.84[EUR][1000 genomes]
rs4680172	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs4680173	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4680174	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4680175	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680176	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4680177	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4680178	0.82[ASN][1000 genomes]
rs4680185	0.88[CHD][hapmap]
rs6440993	0.86[CHD][hapmap]
rs6440994	0.83[CHD][hapmap]
rs6440995	0.83[CHD][hapmap]
rs6762452	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6794214	0.85[CEU][hapmap];0.83[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs6802079	0.91[CHD][hapmap]
rs6807784	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612603	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7615026	0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs7618495	0.86[CHD][hapmap]
rs7619730	0.91[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7627097	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9823946	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs9829532	0.86[CHD][hapmap]
rs9841365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9848852	0.88[CHD][hapmap]
rs9869956	0.93[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv877679	chr3:155128968-155204939	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6440985	PLCH1	cis	parietal	SCAN
rs6440985	SLC33A1	cis	cerebellum	SCAN
rs6440985	KCNAB1	cis	cerebellum	SCAN
rs6440985	GFM1	cis	cerebellum	SCAN
rs6440985	KCNAB1	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:155142200-155146800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr3:155145000-155146000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:155145000-155146400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:155145000-155146400	Weak transcription	Thymus	Thymus
5	chr3:155145200-155146400	Weak transcription	NHEK	skin
6	chr3:155145200-155148200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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