Variant report

Variant	rs148109
Chromosome Location	chr6:54759226-54759227
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	chr6:54758702..54760512-chr6:54764567..54767361,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10456176	0.81[CEU][hapmap]
rs10485136	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs10948866	0.81[CEU][hapmap]
rs10948879	0.81[AMR][1000 genomes]
rs1115159	0.94[CHB][hapmap];0.82[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs1472679	0.81[CEU][hapmap]
rs1503146	0.87[ASN][1000 genomes]
rs1503147	0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs171224	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs181155	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2064432	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs2179786	0.80[CHB][hapmap]
rs2207025	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2207026	0.95[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239779	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239781	0.96[CEU][hapmap];0.80[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239783	0.96[CEU][hapmap];0.80[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs239790	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs239792	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs239794	0.85[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.83[MKK][hapmap]
rs239796	0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs239801	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs239813	0.90[EUR][1000 genomes]
rs239815	0.85[CEU][hapmap]
rs239837	0.87[ASW][hapmap];0.96[CEU][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs239850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239854	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2816810	0.80[CEU][hapmap]
rs2816811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2816812	0.96[CEU][hapmap];0.81[CHB][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4141552	0.94[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs421957	0.85[CEU][hapmap]
rs4712081	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs6459034	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6459035	0.83[ASN][1000 genomes]
rs6937970	0.81[CEU][hapmap]
rs7453866	0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs7741915	0.81[CHB][hapmap];1.00[CHD][hapmap];0.83[MEX][hapmap]
rs9296771	0.88[CHB][hapmap]
rs931766	0.81[CEU][hapmap]
rs932452	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs9367597	0.88[CHB][hapmap];0.85[JPT][hapmap]
rs9370337	0.81[ASN][1000 genomes]
rs9396006	0.85[JPT][hapmap]
rs9396036	0.86[CHB][hapmap]
rs971526	0.81[CEU][hapmap]
rs973205	0.81[CEU][hapmap]
rs988913	0.82[CHD][hapmap]

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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54739800-54763000	Weak transcription	Small Intestine	intestine
2	chr6:54744400-54761000	Weak transcription	Duodenum Mucosa	Duodenum
3	chr6:54757200-54763000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:54757800-54760600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:54757800-54763200	Weak transcription	NHEK	skin
6	chr6:54758000-54761200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:54758000-54769400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:54758000-54775000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:54758400-54761000	Weak transcription	HMEC	breast
10	chr6:54758600-54759600	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr6:54759200-54761000	Weak transcription	Fetal Intestine Small	intestine
12	chr6:54759200-54763000	Weak transcription	Fetal Intestine Large	intestine

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