Variant report

Variant	rs6780388
Chromosome Location	chr3:23404073-23404074
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	chr3:23398268..23400293-chr3:23402710..23405112,2	MCF-7	breast:

Extended variants
information (count: 113 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10510539	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs11129120	0.94[CEU][hapmap]
rs11707450	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs11713090	0.94[CEU][hapmap]
rs11715035	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11718111	0.94[CEU][hapmap]
rs13316118	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs1391756	0.84[CEU][hapmap]
rs1498812	0.94[CEU][hapmap]
rs1692619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1692621	0.94[CEU][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs1692646	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs1692647	0.81[CEU][hapmap]
rs1692648	0.91[JPT][hapmap]
rs1692649	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs1695180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1695183	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs1695185	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs1695192	0.80[CEU][hapmap]
rs1695203	0.81[CEU][hapmap]
rs1695205	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17013268	0.89[CEU][hapmap];0.92[JPT][hapmap]
rs17013425	0.94[CEU][hapmap]
rs17194751	0.94[CEU][hapmap];0.82[JPT][hapmap]
rs17402378	1.00[CEU][hapmap]
rs1874234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1874502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1874503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1994953	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1995175	0.81[CEU][hapmap]
rs2036044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036045	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2047339	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2055155	0.85[CEU][hapmap]
rs2055156	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2055307	0.94[CEU][hapmap]
rs2101811	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[EUR][1000 genomes]
rs2132144	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2132148	1.00[CHB][hapmap]
rs2132149	1.00[CHB][hapmap]
rs2173057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2201484	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2359754	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2359755	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs2359761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs3104242	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4858063	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs4858068	0.97[EUR][1000 genomes]
rs4858070	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858489	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858490	0.87[CEU][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858495	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4858499	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4858507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5023615	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6550758	0.86[EUR][1000 genomes]
rs6550759	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6550760	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6765758	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6790327	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6799132	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6801824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs704535	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73138453	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7614195	0.94[CEU][hapmap]
rs7621680	0.86[EUR][1000 genomes]
rs7629327	0.84[CEU][hapmap]
rs7636705	0.94[CEU][hapmap]
rs7637485	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7643705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646541	0.81[CEU][hapmap]
rs7648425	0.85[CEU][hapmap]
rs7653868	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs778457	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs778458	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs778463	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs778465	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs778469	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs778483	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs778489	0.94[CEU][hapmap];0.92[JPT][hapmap]
rs778492	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs778497	1.00[CEU][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes]
rs778502	1.00[CEU][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs778511	0.94[CEU][hapmap]
rs778513	0.94[CEU][hapmap]
rs778517	0.94[CEU][hapmap]
rs778518	0.94[CEU][hapmap]
rs778519	0.94[CEU][hapmap]
rs778520	0.81[CEU][hapmap]
rs778522	0.94[CEU][hapmap]
rs778524	0.81[CEU][hapmap]
rs778525	0.94[CEU][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes]
rs778527	0.94[CEU][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs801277	0.81[CEU][hapmap]
rs875443	0.94[CEU][hapmap];1.00[YRI][hapmap]
rs931609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9757330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9758590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9815299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9823684	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9836135	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs9840808	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9841336	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9844558	0.93[YRI][hapmap]
rs9848389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9849679	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9863465	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9875910	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014701	chr3:23257658-23416094	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv876624	chr3:23385877-23483536	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv876625	chr3:23390301-23509597	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23398400-23413000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:23398600-23414600	Weak transcription	Psoas Muscle	Psoas
3	chr3:23403800-23404200	Enhancers	Gastric	stomach
4	chr3:23403800-23404200	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr3:23403800-23404400	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr3:23404000-23404400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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