Variant report

Variant	rs16902593
Chromosome Location	chr5:35920057-35920058
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	chr5:35918022..35920429-chr5:35920583..35922848,2	MCF-7	breast:

Extended variants
information (count: 123 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10041865	1.00[EUR][1000 genomes]
rs10058723	1.00[EUR][1000 genomes]
rs10058960	1.00[EUR][1000 genomes]
rs10077553	1.00[EUR][1000 genomes]
rs10079269	1.00[EUR][1000 genomes]
rs10079517	1.00[EUR][1000 genomes]
rs10491432	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10491433	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11567717	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11567730	1.00[EUR][1000 genomes]
rs11567764	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11951270	1.00[EUR][1000 genomes]
rs1374015	1.00[EUR][1000 genomes]
rs1494570	1.00[EUR][1000 genomes]
rs16902514	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16902535	1.00[EUR][1000 genomes]
rs16902557	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16902562	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16902592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16902594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16902638	1.00[EUR][1000 genomes]
rs16902639	1.00[EUR][1000 genomes]
rs16902643	1.00[EUR][1000 genomes]
rs16902650	1.00[EUR][1000 genomes]
rs16902651	1.00[EUR][1000 genomes]
rs16902667	1.00[EUR][1000 genomes]
rs16902670	1.00[EUR][1000 genomes]
rs16902682	1.00[EUR][1000 genomes]
rs28756345	1.00[EUR][1000 genomes]
rs55662701	1.00[EUR][1000 genomes]
rs56053392	1.00[EUR][1000 genomes]
rs56169453	1.00[EUR][1000 genomes]
rs56276485	1.00[EUR][1000 genomes]
rs56665523	1.00[EUR][1000 genomes]
rs56773364	1.00[EUR][1000 genomes]
rs57273729	1.00[EUR][1000 genomes]
rs57498894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57579833	1.00[EUR][1000 genomes]
rs58168401	1.00[EUR][1000 genomes]
rs58457055	1.00[EUR][1000 genomes]
rs58671818	1.00[EUR][1000 genomes]
rs58872016	1.00[EUR][1000 genomes]
rs59555387	1.00[EUR][1000 genomes]
rs59714026	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6451222	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6861184	1.00[EUR][1000 genomes]
rs6864736	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6875303	1.00[EUR][1000 genomes]
rs6876261	1.00[EUR][1000 genomes]
rs6881747	1.00[EUR][1000 genomes]
rs6881919	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6894309	1.00[EUR][1000 genomes]
rs73076116	1.00[EUR][1000 genomes]
rs73076118	1.00[EUR][1000 genomes]
rs73076126	1.00[EUR][1000 genomes]
rs73076137	1.00[EUR][1000 genomes]
rs73076149	1.00[EUR][1000 genomes]
rs73076151	1.00[EUR][1000 genomes]
rs73076155	1.00[EUR][1000 genomes]
rs73076161	1.00[EUR][1000 genomes]
rs73076166	1.00[EUR][1000 genomes]
rs73076168	1.00[EUR][1000 genomes]
rs73076171	1.00[EUR][1000 genomes]
rs73076172	1.00[EUR][1000 genomes]
rs73076173	1.00[EUR][1000 genomes]
rs73076178	1.00[EUR][1000 genomes]
rs73076180	1.00[EUR][1000 genomes]
rs73076197	1.00[EUR][1000 genomes]
rs73076199	1.00[EUR][1000 genomes]
rs73078005	1.00[EUR][1000 genomes]
rs73078010	1.00[EUR][1000 genomes]
rs73078011	1.00[EUR][1000 genomes]
rs73078024	1.00[EUR][1000 genomes]
rs73086208	1.00[EUR][1000 genomes]
rs73086212	1.00[EUR][1000 genomes]
rs73086213	1.00[EUR][1000 genomes]
rs73086237	1.00[EUR][1000 genomes]
rs73086243	1.00[EUR][1000 genomes]
rs73086251	1.00[EUR][1000 genomes]
rs73086261	1.00[EUR][1000 genomes]
rs73086281	1.00[EUR][1000 genomes]
rs73086282	1.00[EUR][1000 genomes]
rs73086302	1.00[EUR][1000 genomes]
rs73088209	1.00[EUR][1000 genomes]
rs73088244	1.00[EUR][1000 genomes]
rs73090209	1.00[EUR][1000 genomes]
rs73090222	1.00[EUR][1000 genomes]
rs73090239	1.00[EUR][1000 genomes]
rs73090241	1.00[EUR][1000 genomes]
rs73090248	1.00[EUR][1000 genomes]
rs73090257	1.00[EUR][1000 genomes]
rs73090276	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090284	1.00[EUR][1000 genomes]
rs73090289	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090291	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090295	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73090298	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73092011	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73092033	1.00[EUR][1000 genomes]
rs73092034	1.00[EUR][1000 genomes]
rs73092092	1.00[EUR][1000 genomes]
rs73092100	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094009	1.00[EUR][1000 genomes]
rs73094019	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73094022	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7701519	1.00[EUR][1000 genomes]
rs7704710	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7708334	1.00[EUR][1000 genomes]
rs7710405	1.00[EUR][1000 genomes]
rs7714297	1.00[EUR][1000 genomes]
rs7720394	1.00[EUR][1000 genomes]
rs7724777	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs852244	0.89[AFR][1000 genomes]
rs852246	0.89[AFR][1000 genomes]
rs852251	0.89[AFR][1000 genomes]
rs852252	0.89[AFR][1000 genomes]
rs860414	0.89[AFR][1000 genomes]
rs863781	0.89[AFR][1000 genomes]
rs9292610	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471011	chr5:35861068-36003217	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830261	chr5:35863084-36018048	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1025695	chr5:35902486-36036934	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv4794	chr5:35906690-35934205	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16902593	RNF212	trans	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:35915600-35924200	Weak transcription	Primary T cells from cord blood	blood
2	chr5:35918400-35920200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:35918600-35920400	Enhancers	Muscle Satellite Cultured Cells	--
4	chr5:35918600-35920800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr5:35918800-35920200	Enhancers	Hela-S3	cervix
6	chr5:35918800-35920200	Enhancers	HMEC	breast
7	chr5:35918800-35920200	Enhancers	HSMM	muscle
8	chr5:35918800-35920200	Enhancers	NHDF-Ad	bronchial
9	chr5:35919000-35920400	Enhancers	NHLF	lung
10	chr5:35919400-35920800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:35919600-35920400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr5:35919600-35920600	ZNF genes & repeats	Dnd41	blood
13	chr5:35919600-35921000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:35919600-35924200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr5:35919800-35920400	ZNF genes & repeats	NHEK	skin
16	chr5:35919800-35921400	ZNF genes & repeats	Fetal Thymus	thymus
17	chr5:35920000-35920200	ZNF genes & repeats	Thymus	Thymus
18	chr5:35920000-35923400	Weak transcription	Osteobl	bone
19	chr5:35920000-35924000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:35920000-35924200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr5:35920000-35924600	Weak transcription	HSMMtube	muscle

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