Variant report

Variant	rs10779227
Chromosome Location	chr12:86446813-86446814
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr12:86446638-86446926	T-47D	breast:	n/a	chr12:86446768-86446780

Variant related genes	Relation type
MGAT4C	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10746359	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10779224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10779225	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10779236	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10863128	0.91[ASN][1000 genomes]
rs10863129	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10863131	0.83[ASN][1000 genomes]
rs10863139	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10863141	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs10863149	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10863164	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11117148	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11117149	0.83[ASN][1000 genomes]
rs11117150	0.83[ASN][1000 genomes]
rs11117152	0.96[CEU][hapmap];1.00[CHB][hapmap]
rs11117154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap]
rs11117162	0.88[LWK][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs11513955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11611607	0.92[AFR][1000 genomes]
rs11614214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12298516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs1354258	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs1493407	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1502803	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs1698754	0.83[CEU][hapmap]
rs1847206	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35629197	0.83[AFR][1000 genomes]
rs61929393	0.83[AFR][1000 genomes]
rs61929399	0.92[AFR][1000 genomes]
rs61929424	0.92[AFR][1000 genomes]
rs61931064	0.83[ASN][1000 genomes]
rs61931120	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61931121	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61931135	0.86[ASN][1000 genomes]
rs6539944	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6539947	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7136221	1.00[CEU][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs721829	0.83[ASN][1000 genomes]
rs7294859	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7295033	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7302043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap]
rs7307686	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73177179	0.83[AFR][1000 genomes]
rs7398950	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7485853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7486591	1.00[CEU][hapmap]
rs7489114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap]
rs7961367	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHD][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7965726	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs7971447	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs839091	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs839135	0.84[CEU][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs839181	0.80[ASN][1000 genomes]
rs9668994	1.00[YRI][hapmap]
rs9669353	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9706029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[TSI][hapmap]
rs9738989	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9804820	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv832476	chr12:86389751-86497122	Enhancers ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	nsv798	chr12:86399822-86447451	ZNF genes & repeats Enhancers Weak transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
4	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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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