Variant report

Variant	rs61139258
Chromosome Location	chr15:55703437-55703438
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	chr15:55701169..55703678-chr15:55710788..55712535,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10450983	0.93[EUR][1000 genomes]
rs10518810	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11732	0.84[AMR][1000 genomes]
rs13329586	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs16953240	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs16976307	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs16976314	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2414412	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28378485	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28413009	0.84[AFR][1000 genomes]
rs28483325	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28636929	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs28653717	0.84[AMR][1000 genomes]
rs3203152	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs34482650	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55706848	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs56340826	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs56760921	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57489605	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs57648583	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs57809907	0.90[AFR][1000 genomes]
rs58013690	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs58053176	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58220352	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58447274	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58507025	0.85[AFR][1000 genomes]
rs58550265	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs58581371	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs58734748	0.81[AFR][1000 genomes]
rs58743089	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs59562815	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs59742963	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60071399	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs60925254	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs61069460	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6493780	0.84[AMR][1000 genomes]
rs6493781	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7162724	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7164158	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7164984	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7168455	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7168869	0.89[EUR][1000 genomes]
rs7168882	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7169460	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs7170157	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7170970	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7171766	1.00[EUR][1000 genomes]
rs7173562	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7174313	0.82[EUR][1000 genomes]
rs7176013	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7177113	0.93[EUR][1000 genomes]
rs7177362	0.93[EUR][1000 genomes]
rs7177888	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7181226	0.86[AFR][1000 genomes]
rs7181805	0.90[AFR][1000 genomes]
rs7183937	1.00[EUR][1000 genomes]
rs73406912	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73406921	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73406928	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73406986	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs73408805	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs73408809	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs73408825	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73421623	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73421633	0.88[AMR][1000 genomes]
rs73421665	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs74015572	0.84[AMR][1000 genomes]
rs8023354	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8026454	0.84[AMR][1000 genomes]
rs8027135	0.84[AMR][1000 genomes]
rs8028482	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8028763	0.80[EUR][1000 genomes]
rs8029077	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs8029258	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8031507	0.88[AMR][1000 genomes]
rs8034029	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8040840	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8041044	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8041349	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8041382	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8041885	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs8042642	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8043415	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv904243	chr15:55627528-55734158	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv520799	chr15:55645661-55760522	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv1041635	chr15:55658171-55943942	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv904244	chr15:55687969-55770911	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61139258	CCPG1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55701200-55713800	Weak transcription	Ovary	ovary
2	chr15:55701400-55712400	Weak transcription	HSMMtube	muscle
3	chr15:55701400-55713200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr15:55701600-55713200	Weak transcription	Brain Angular Gyrus	brain
5	chr15:55701600-55715000	Weak transcription	Pancreas	Pancrea
6	chr15:55701600-55729800	Weak transcription	Fetal Stomach	stomach
7	chr15:55701800-55711400	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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