Variant report

Variant	rs4869320
Chromosome Location	chr5:96520606-96520607
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:96505549..96507976-chr5:96519747..96521338,2	MCF-7	breast:
2	chr5:96519642..96521582-chr5:96527509..96529068,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2544771	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2544772	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2548319	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28484279	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs31000	0.92[EUR][1000 genomes]
rs31002	0.87[EUR][1000 genomes]
rs31004	0.86[EUR][1000 genomes]
rs316195	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4869150	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57726714	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432755	chr5:95987984-96657483	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv598962	chr5:96057891-96893164	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv830412	chr5:96427305-96606619	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1019790	chr5:96471680-96980633	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv537812	chr5:96471680-96980633	ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv882391	chr5:96496189-96533469	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv882392	chr5:96496189-96546238	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv882393	chr5:96496189-96567950	Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4869320	RIOK2	cis	Nerve Tibial	GTEx
rs4869320	RIOK2	Cis_1M	lymphoblastoid	RTeQTL
rs4869320	RIOK2	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96519200-96526200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:96519800-96521800	Enhancers	HepG2	liver
3	chr5:96520000-96521200	Weak transcription	Duodenum Mucosa	Duodenum
4	chr5:96520000-96521400	Weak transcription	Primary B cells from cord blood	blood
5	chr5:96520000-96521400	Weak transcription	Ovary	ovary
6	chr5:96520000-96521600	Enhancers	Fetal Intestine Large	intestine
7	chr5:96520000-96522800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:96520000-96523200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr5:96520000-96528200	Weak transcription	NHEK	skin
10	chr5:96520000-96531600	Weak transcription	HSMM	muscle
11	chr5:96520000-96534800	Weak transcription	Left Ventricle	heart
12	chr5:96520200-96520800	Weak transcription	Pancreas	Pancrea
13	chr5:96520200-96521000	Weak transcription	Fetal Brain Female	brain
14	chr5:96520200-96521200	Weak transcription	Liver	Liver
15	chr5:96520200-96521200	Weak transcription	Fetal Intestine Small	intestine
16	chr5:96520200-96523200	Weak transcription	Lung	lung
17	chr5:96520200-96524600	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:96520200-96524800	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr5:96520400-96520800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:96520400-96520800	Weak transcription	Psoas Muscle	Psoas
21	chr5:96520400-96521000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:96520400-96521400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:96520600-96521000	Enhancers	Dnd41	blood

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