Variant report

Variant	rs16881303
Chromosome Location	chr5:52629643-52629644
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	chr5:52629610..52631270-chr5:52660976..52663491,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs13153694	1.00[EUR][1000 genomes]
rs13156370	1.00[EUR][1000 genomes]
rs13158674	1.00[EUR][1000 genomes]
rs13159322	1.00[EUR][1000 genomes]
rs13171311	1.00[EUR][1000 genomes]
rs13179965	1.00[EUR][1000 genomes]
rs13180278	1.00[EUR][1000 genomes]
rs34645246	1.00[EUR][1000 genomes]
rs34779217	1.00[EUR][1000 genomes]
rs34951553	1.00[EUR][1000 genomes]
rs34953700	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35285333	1.00[EUR][1000 genomes]
rs35384598	1.00[EUR][1000 genomes]
rs35412043	1.00[EUR][1000 genomes]
rs35689181	1.00[EUR][1000 genomes]
rs71619950	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71633454	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv830297	chr5:52492494-52707758	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1020388	chr5:52607736-52637122	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a
5	nsv1016368	chr5:52607736-52640986	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16881303	PNLDC1	trans	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52620200-52633600	Weak transcription	Esophagus	oesophagus
2	chr5:52626000-52631600	Enhancers	NHLF	lung
3	chr5:52626000-52640000	Enhancers	HMEC	breast
4	chr5:52626200-52631600	Enhancers	NHDF-Ad	bronchial
5	chr5:52626400-52631800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:52626600-52631600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:52626800-52631600	Enhancers	Osteobl	bone
8	chr5:52628400-52631200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:52628600-52629800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:52628800-52631400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:52629000-52631400	Enhancers	Aorta	Aorta
12	chr5:52629000-52631600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:52629000-52631600	Enhancers	Hela-S3	cervix
14	chr5:52629000-52631600	Enhancers	HSMM	muscle
15	chr5:52629200-52629800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:52629200-52630600	Enhancers	HSMMtube	muscle
17	chr5:52629200-52631400	Enhancers	NH-A	brain
18	chr5:52629200-52632000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr5:52629400-52630400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr5:52629600-52630000	Flanking Active TSS	NHEK	skin
21	chr5:52629600-52630400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr5:52629600-52632000	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr5:52629600-52634000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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