Variant report

Variant	rs9496346
Chromosome Location	chr6:142669338-142669339
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:142667887..142670246-chr6:142675631..142677996,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1040525	0.87[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1040526	0.94[CEU][hapmap];0.95[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1342060	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1360194	0.94[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1418201	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs155259	0.82[EUR][1000 genomes]
rs1891308	0.84[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2039986	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2039987	0.88[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes]
rs2050157	0.82[ASW][hapmap];0.84[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2294764	0.94[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2294771	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs262119	0.82[EUR][1000 genomes]
rs262121	0.82[EUR][1000 genomes]
rs262129	0.82[EUR][1000 genomes]
rs263178	0.80[EUR][1000 genomes]
rs263179	0.80[EUR][1000 genomes]
rs263180	0.82[EUR][1000 genomes]
rs263181	0.82[EUR][1000 genomes]
rs263182	0.82[EUR][1000 genomes]
rs263183	0.82[EUR][1000 genomes]
rs263184	0.82[EUR][1000 genomes]
rs263186	0.82[EUR][1000 genomes]
rs263187	0.82[EUR][1000 genomes]
rs263188	0.82[EUR][1000 genomes]
rs263189	0.82[EUR][1000 genomes]
rs3748069	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3817929	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4896582	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs6570507	0.84[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6570508	0.81[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs6570509	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6570510	0.82[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6909857	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6929442	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6937121	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7741741	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7753012	0.95[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap]
rs7754638	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7755109	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7756305	0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs7763064	0.87[EUR][1000 genomes]
rs7770386	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7774095	0.90[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7776375	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9373346	0.83[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9389984	0.92[EUR][1000 genomes]
rs9389985	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9389986	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9389987	0.91[EUR][1000 genomes]
rs9399401	0.94[CEU][hapmap];0.85[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9403380	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9403381	0.84[CEU][hapmap];0.86[CHB][hapmap];0.97[GIH][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9403382	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403383	0.94[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9403387	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9496369	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9496374	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9496392	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs962554	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs972982	0.81[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949088	chr6:142561402-143128849	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv830825	chr6:142585242-142752575	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142654800-142676600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:142657400-142678800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:142663400-142676400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:142665600-142680200	Weak transcription	HUVEC	blood vessel
5	chr6:142666000-142670200	Weak transcription	A549	lung
6	chr6:142666000-142677000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:142666800-142670400	Weak transcription	Liver	Liver
8	chr6:142667400-142674800	Weak transcription	Fetal Lung	lung
9	chr6:142668600-142669400	Enhancers	HepG2	liver

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