Variant report

Variant	rs12652878
Chromosome Location	chr5:60164776-60164777
allele	C/T
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	POLR2A	chr5:60164649-60164830	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000272308	TF binding region

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1021005	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10805374	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10939879	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11739952	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11740632	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12516995	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12517310	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12518404	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12518792	0.80[EUR][1000 genomes]
rs12652830	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12653132	0.80[EUR][1000 genomes]
rs12654306	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12655209	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12655603	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1382917	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1471488	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1479645	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1526896	0.80[EUR][1000 genomes]
rs17332824	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17392014	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17419290	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17444495	0.82[EUR][1000 genomes]
rs1983484	0.81[EUR][1000 genomes]
rs2049579	0.81[EUR][1000 genomes]
rs2120956	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2120957	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28436304	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2898309	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34741733	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3797559	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4642318	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4647052	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4647132	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4647137	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4647150	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700397	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4700399	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4700402	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4700404	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4700407	0.82[EUR][1000 genomes]
rs55738840	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55814394	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56025209	0.81[EUR][1000 genomes]
rs56031340	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56284222	0.80[EUR][1000 genomes]
rs56350217	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs58078456	0.92[ASN][1000 genomes]
rs58646987	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60858663	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61017995	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61101592	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62365455	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62365458	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62367862	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62367872	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62367878	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62367879	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62367885	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62367903	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62372102	0.88[ASN][1000 genomes]
rs62372103	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62372133	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62372134	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6449512	0.90[EUR][1000 genomes]
rs67490467	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67555188	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67858932	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6884966	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs726824	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72757187	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72759206	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72759215	0.80[EUR][1000 genomes]
rs7701398	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709522	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7713481	0.81[EUR][1000 genomes]
rs7714396	0.87[EUR][1000 genomes]
rs7722373	0.88[ASN][1000 genomes]
rs7723349	0.86[ASN][1000 genomes]
rs7723901	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7737276	0.80[EUR][1000 genomes]
rs868791	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs888799	0.81[EUR][1000 genomes]
rs9687099	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs976630	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs976631	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492277	chr5:59905195-60180834	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv934153	chr5:60004982-60309751	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv949662	chr5:60047974-60488379	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1017095	chr5:60050600-60414783	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv933326	chr5:60074031-60413061	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv881712	chr5:60116613-60266875	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv881713	chr5:60116613-60305125	Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv598305	chr5:60116613-60308836	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv881714	chr5:60116613-60313015	Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv881715	chr5:60116613-60356423	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	nsv598306	chr5:60129361-60266875	Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv598307	chr5:60129361-60308836	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv881716	chr5:60129361-60313015	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv462199	chr5:60129361-60329624	Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv598308	chr5:60129361-60329624	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
16	nsv462200	chr5:60135985-60266875	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv598309	chr5:60135985-60266875	Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv598310	chr5:60135985-60308836	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
19	nsv598311	chr5:60136626-60308836	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv520871	chr5:60141245-60320157	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv881717	chr5:60141245-60372582	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv598312	chr5:60147754-60313015	Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
23	nsv881718	chr5:60147754-60313015	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12652878	DEPDC1B	Cis_1M	lymphoblastoid	RTeQTL
rs12652878	ERCC8	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:60162600-60166800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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