Variant report

Variant	rs6957232
Chromosome Location	chr7:80732690-80732691
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:80545333..80552381-chr7:80731206..80734904,6	MCF-7	breast:
2	chr7:80545954..80551359-chr7:80730647..80734192,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075223	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10225640	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10234328	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10239474	0.90[ASN][1000 genomes]
rs10245648	0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10247169	0.86[CEU][hapmap];0.83[JPT][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs10265745	0.91[EUR][1000 genomes]
rs10267251	0.89[EUR][1000 genomes]
rs10274106	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10276120	0.90[EUR][1000 genomes]
rs10480510	0.92[EUR][1000 genomes]
rs10480511	0.93[EUR][1000 genomes]
rs10480852	0.92[EUR][1000 genomes]
rs10480853	0.91[EUR][1000 genomes]
rs12533994	0.86[EUR][1000 genomes]
rs12534374	0.83[JPT][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs12538859	0.85[GIH][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs12540085	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12540330	0.92[EUR][1000 genomes]
rs13221460	0.92[EUR][1000 genomes]
rs13240198	0.85[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs1528736	0.83[ASN][1000 genomes]
rs17154740	0.82[GIH][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs1919369	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2247480	0.93[EUR][1000 genomes]
rs2247579	0.93[EUR][1000 genomes]
rs2697221	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2697222	0.81[EUR][1000 genomes]
rs2697224	0.93[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2697225	0.93[CEU][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2697227	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2697943	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs2697944	0.81[EUR][1000 genomes]
rs2697945	0.81[EUR][1000 genomes]
rs2697946	0.81[EUR][1000 genomes]
rs28401278	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs28536573	0.90[AFR][1000 genomes]
rs28796047	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34344876	0.89[ASN][1000 genomes]
rs35758038	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35876610	0.90[ASN][1000 genomes]
rs3843546	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3891957	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3891958	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3902760	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4540349	0.91[EUR][1000 genomes]
rs4573183	0.90[EUR][1000 genomes]
rs4732107	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4732109	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58692795	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61059308	0.90[ASN][1000 genomes]
rs62465327	0.87[EUR][1000 genomes]
rs62467389	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6951995	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6955164	0.86[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6959189	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6969190	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6969953	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6971951	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6973162	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73384423	0.91[AFR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7786639	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs953190	0.92[EUR][1000 genomes]
rs953191	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];0.90[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
rs6957232	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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