Variant report

Variant	rs2697225
Chromosome Location	chr7:80723727-80723728
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:80547954..80550171-chr7:80721160..80725136,3	MCF-7	breast:
2	chr7:80722580..80725248-chr7:80741058..80743556,2	MCF-7	breast:
3	chr7:80550844..80552775-chr7:80722519..80724746,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075223	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10225640	0.95[EUR][1000 genomes]
rs10234328	0.92[EUR][1000 genomes]
rs10245648	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10247169	0.93[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10265624	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10265745	0.91[EUR][1000 genomes]
rs10267251	0.89[EUR][1000 genomes]
rs10274106	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10276120	0.90[EUR][1000 genomes]
rs10277984	0.87[ASN][1000 genomes]
rs10480510	0.92[EUR][1000 genomes]
rs10480511	0.91[EUR][1000 genomes]
rs10480852	0.81[JPT][hapmap];0.92[EUR][1000 genomes]
rs10480853	0.91[EUR][1000 genomes]
rs12533994	0.86[EUR][1000 genomes]
rs12534374	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.85[TSI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12538859	0.81[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs12540085	0.91[EUR][1000 genomes]
rs12540330	0.92[EUR][1000 genomes]
rs13221460	0.92[EUR][1000 genomes]
rs13240198	0.81[GIH][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs17154740	0.81[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs1919369	0.90[EUR][1000 genomes]
rs2247480	0.92[EUR][1000 genomes]
rs2247579	0.92[EUR][1000 genomes]
rs2697221	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697222	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697227	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2697943	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697944	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697945	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697946	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28401278	0.81[EUR][1000 genomes]
rs28627226	0.87[ASN][1000 genomes]
rs28715268	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28731315	0.87[ASN][1000 genomes]
rs28796047	0.93[EUR][1000 genomes]
rs35758038	0.92[EUR][1000 genomes]
rs3843546	0.93[EUR][1000 genomes]
rs3891957	0.92[EUR][1000 genomes]
rs3891958	0.92[EUR][1000 genomes]
rs3902760	0.88[EUR][1000 genomes]
rs4540349	0.89[EUR][1000 genomes]
rs4573183	0.90[EUR][1000 genomes]
rs4732106	0.87[ASN][1000 genomes]
rs4732107	0.92[EUR][1000 genomes]
rs4732109	0.91[EUR][1000 genomes]
rs58692795	0.92[EUR][1000 genomes]
rs62465327	0.87[EUR][1000 genomes]
rs62467389	0.93[EUR][1000 genomes]
rs6467564	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs6467574	0.88[ASN][1000 genomes]
rs6951995	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6955164	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6957232	0.93[CEU][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6959189	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6969190	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6971951	0.95[EUR][1000 genomes]
rs6973162	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73384423	0.92[EUR][1000 genomes]
rs7786639	0.92[EUR][1000 genomes]
rs7790887	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs949733	0.87[ASN][1000 genomes]
rs953190	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs953191	0.92[EUR][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
rs2697225	SEMA3C	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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