Variant report

Variant	rs12538859
Chromosome Location	chr7:80703613-80703614
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:80570369..80572451-chr7:80702280..80705942,3	MCF-7	breast:
2	chr7:80569413..80574847-chr7:80699987..80704923,10	MCF-7	breast:
3	chr7:80546160..80553330-chr7:80697243..80707851,28	MCF-7	breast:
4	chr7:80545266..80555113-chr7:80701488..80708340,14	MCF-7	breast:
5	chr7:80697644..80700477-chr7:80703389..80704968,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075223	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10225640	0.89[EUR][1000 genomes]
rs10234328	0.86[EUR][1000 genomes]
rs10245648	0.92[EUR][1000 genomes]
rs10247169	0.81[JPT][hapmap];0.80[TSI][hapmap]
rs10265745	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10267251	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10274106	0.90[EUR][1000 genomes]
rs10276120	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10277023	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10480510	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10480511	0.93[CEU][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10480852	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10480853	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12533994	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12534374	0.81[JPT][hapmap]
rs12540085	0.85[EUR][1000 genomes]
rs12540330	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13221460	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13240198	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1528390	1.00[YRI][hapmap]
rs1528391	1.00[YRI][hapmap]
rs17154740	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1881541	0.93[ASW][hapmap];0.97[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs1919369	0.82[EUR][1000 genomes]
rs2247480	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2247579	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2697219	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2697221	0.93[EUR][1000 genomes]
rs2697224	0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs2697225	0.81[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs2697227	0.85[EUR][1000 genomes]
rs28796047	0.85[EUR][1000 genomes]
rs35758038	0.86[EUR][1000 genomes]
rs3843546	0.85[EUR][1000 genomes]
rs3891957	0.86[EUR][1000 genomes]
rs3891958	0.86[EUR][1000 genomes]
rs3902760	0.82[EUR][1000 genomes]
rs4540349	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4573183	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4732107	0.86[EUR][1000 genomes]
rs4732109	0.85[EUR][1000 genomes]
rs58692795	0.86[EUR][1000 genomes]
rs62465327	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62467389	0.85[EUR][1000 genomes]
rs6467539	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6944056	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs6951995	0.89[EUR][1000 genomes]
rs6955164	0.85[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs6957232	0.85[GIH][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs6959189	0.93[EUR][1000 genomes]
rs6969190	0.89[EUR][1000 genomes]
rs6971951	0.89[EUR][1000 genomes]
rs6973162	0.93[EUR][1000 genomes]
rs73384423	0.86[EUR][1000 genomes]
rs7786639	0.86[EUR][1000 genomes]
rs7806015	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs953190	0.86[EUR][1000 genomes]
rs953191	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv888524	chr7:80107798-80723062	Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	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
3	nsv888551	chr7:80620397-80723062	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12538859	SEMA3C	cis	parietal	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:80700600-80703800	Weak transcription	Pancreas	Pancrea
2	chr7:80700800-80704000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:80701000-80704400	Weak transcription	Osteobl	bone
4	chr7:80702200-80705200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:80702200-80705200	Enhancers	HMEC	breast
6	chr7:80702800-80705000	Enhancers	Fetal Muscle Leg	muscle
7	chr7:80702800-80705600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:80703000-80704000	Enhancers	HSMM	muscle
9	chr7:80703000-80704800	Enhancers	NH-A	brain
10	chr7:80703000-80705400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:80703400-80704200	Enhancers	NHEK	skin
12	chr7:80703600-80704400	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr7:80703600-80704600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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