Variant report

Variant	rs12668893
Chromosome Location	chr7:80748647-80748648
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	chr7:80748132..80750637-chr7:80752340..80754358,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10239474	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10247169	0.86[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10265624	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10274106	0.83[ASN][1000 genomes]
rs10277023	0.90[EUR][1000 genomes]
rs10277984	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12534374	0.82[CHD][hapmap];0.82[JPT][hapmap]
rs12538655	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12538859	0.80[TSI][hapmap]
rs13240198	0.80[TSI][hapmap]
rs1528736	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17154740	0.80[TSI][hapmap]
rs2697219	0.90[EUR][1000 genomes]
rs2697222	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2697224	0.82[JPT][hapmap]
rs2697225	0.84[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap]
rs2697943	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2697944	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2697945	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2697946	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28715268	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34344876	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35876610	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3914074	0.90[AFR][1000 genomes]
rs4732106	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61059308	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6467574	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67243095	0.82[EUR][1000 genomes]
rs6955164	0.84[CHD][hapmap];0.82[JPT][hapmap];0.92[TSI][hapmap]
rs6957232	0.92[TSI][hapmap]
rs7790887	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs949733	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs953190	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034690	chr7:80520004-80987682	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv888552	chr7:80683308-80755310	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv888553	chr7:80683308-80766407	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv888554	chr7:80695828-80755310	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv888555	chr7:80695828-80766407	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv888556	chr7:80695828-80797794	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv831044	chr7:80721773-80918591	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12668893	SEMA3C	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80742400-80748800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr7:80745200-80762600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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