Variant report

Variant	rs28484279
Chromosome Location	chr5:96519851-96519852
allele	A/G
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	TCF12	chr5:96518453-96520006	A549	lung:	n/a	n/a
2	POLR2A	chr5:96517775-96519865	IMR90	lung:	n/a	n/a
3	RCOR1	chr5:96518693-96519909	GM12878	blood:	n/a	n/a
4	NR2F2	chr5:96518693-96519939	K562	blood:	n/a	n/a
5	POLR2A	chr5:96518517-96519856	GM12892	blood:	n/a	n/a
6	ZNF384	chr5:96518717-96519863	K562	blood:	n/a	n/a
7	RFX5	chr5:96518909-96519860	K562	blood:	n/a	n/a
8	KAP1	chr5:96518584-96519952	U2OS	brain:	n/a	n/a
9	MTA3	chr5:96518406-96519986	GM12878	blood:	n/a	n/a
10	REST	chr5:96518200-96520015	H1-neurons	neurons:	n/a	n/a
11	MAX	chr5:96518609-96520013	HepG2	liver:	n/a	n/a
12	POLR2A	chr5:96518531-96519932	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr5:96518512-96519904	GM12878	blood:	n/a	n/a
14	PML	chr5:96518511-96519970	GM12878	blood:	n/a	n/a
15	BCLAF1	chr5:96519046-96519886	GM12878	blood:	n/a	n/a
16	CBX3	chr5:96518715-96519982	K562	blood:	n/a	n/a
17	MAX	chr5:96518444-96520085	A549	lung:	n/a	n/a
18	RCOR1	chr5:96518605-96519931	K562	blood:	n/a	n/a
19	HCFC1	chr5:96518495-96520248	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr5:96518573-96519895	Raji	blood:	n/a	n/a
21	MAX	chr5:96518723-96519922	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:96518566-96520222	MCF10A-Er-Src	breast:	n/a	n/a
23	GABPA	chr5:96518660-96519879	MCF-7	breast:	n/a	chr5:96518997-96519006 chr5:96519507-96519521 chr5:96519510-96519524 chr5:96519510-96519521 chr5:96518997-96519011 chr5:96519463-96519477 chr5:96519415-96519429 chr5:96518997-96519008
24	MAX	chr5:96518624-96519922	MCF-7	breast:	n/a	n/a
25	BCL3	chr5:96518637-96519903	A549	lung:	n/a	n/a
26	CBX3	chr5:96518760-96519934	K562	blood:	n/a	n/a
27	MAX	chr5:96518574-96519937	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr5:96518545-96520166	SK-N-MC	brain:	n/a	n/a
29	E2F6	chr5:96518727-96519973	K562	blood:	n/a	chr5:96518998-96519007 chr5:96519511-96519520
30	POLR2A	chr5:96518317-96519919	U87	brain:	n/a	n/a
31	POLR2A	chr5:96518517-96519905	HepG2	liver:	n/a	n/a
32	TEAD4	chr5:96518647-96520014	HepG2	liver:	n/a	n/a
33	MYBL2	chr5:96518597-96519873	HepG2	liver:	n/a	n/a
34	MAX	chr5:96518577-96519917	HepG2	liver:	n/a	n/a
35	E2F6	chr5:96518739-96519971	H1-hESC	embryonic stem cell:	n/a	chr5:96518998-96519007 chr5:96519511-96519520
36	E2F6	chr5:96518652-96520143	H1-hESC	embryonic stem cell:	n/a	chr5:96518998-96519007 chr5:96519511-96519520
37	NRF1	chr5:96517862-96519926	SK-N-SH	brain:	n/a	chr5:96518997-96519006 chr5:96519507-96519521 chr5:96519417-96519428 chr5:96519510-96519524 chr5:96519510-96519521 chr5:96518997-96519011 chr5:96519463-96519477 chr5:96519415-96519429 chr5:96518997-96519008
38	MXI1	chr5:96517903-96520065	SK-N-SH	brain:	n/a	n/a
39	MTA3	chr5:96518577-96519867	GM12878	blood:	n/a	n/a
40	MAX	chr5:96518641-96519943	H1-hESC	embryonic stem cell:	n/a	n/a
41	STAT5A	chr5:96518560-96519865	GM12878	blood:	n/a	chr5:96519127-96519135
42	SIN3AK20	chr5:96518682-96519893	MCF-7	breast:	n/a	n/a
43	MYC	chr5:96518496-96519883	K562	blood:	n/a	n/a
44	MAX	chr5:96518570-96519922	MCF-7	breast:	n/a	n/a
45	POLR2A	chr5:96518589-96519914	MCF-7	breast:	n/a	n/a
46	SIN3AK20	chr5:96518485-96519995	MCF-7	breast:	n/a	n/a
47	POLR2A	chr5:96518545-96519858	GM12878	blood:	n/a	n/a
48	SETDB1	chr5:96518914-96519895	U2OS	brain:	n/a	chr5:96518998-96519007 chr5:96519511-96519520
49	POLR2A	chr5:96518566-96519908	MCF-7	breast:	n/a	n/a
50	NFIC	chr5:96518646-96519862	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:96505549..96507976-chr5:96519747..96521338,2	MCF-7	breast:
2	chr5:96508014..96513294-chr5:96513654..96520413,9	K562	blood:
3	chr5:96519642..96521582-chr5:96527509..96529068,2	MCF-7	breast:

Variant related genes	Relation type
RIOK2	TF binding region
ENSG00000206698	Chromatin interaction

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

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

rs_ID	r²[population]
rs2544771	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2544772	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2548319	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs31000	0.92[EUR][1000 genomes]
rs31002	0.87[EUR][1000 genomes]
rs31004	0.86[EUR][1000 genomes]
rs316195	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4869150	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4869320	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57726714	0.88[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
rs28484279	RIOK2	cis	Nerve Tibial	GTEx
rs28484279	RIOK2	cis	Artery Tibial	GTEx
rs28484279	RIOK2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:96516600-96520200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:96517200-96520000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:96517200-96520200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:96517400-96520000	Active TSS	Aorta	Aorta
5	chr5:96517400-96520000	Active TSS	Psoas Muscle	Psoas
6	chr5:96517400-96520000	Active TSS	HSMMtube	muscle
7	chr5:96517600-96520000	Active TSS	Ovary	ovary
8	chr5:96517600-96520000	Active TSS	Right Ventricle	heart
9	chr5:96517600-96520000	Active TSS	NHDF-Ad	bronchial
10	chr5:96517800-96520000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:96518200-96520000	Active TSS	Brain Angular Gyrus	brain
12	chr5:96518200-96520000	Active TSS	Brain Germinal Matrix	brain
13	chr5:96518200-96520000	Active TSS	Stomach Mucosa	stomach
14	chr5:96518200-96520000	Active TSS	Stomach Smooth Muscle	stomach
15	chr5:96518200-96520200	Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr5:96518200-96520200	Active TSS	Colonic Mucosa	Colon
17	chr5:96518200-96520200	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr5:96518200-96520200	Active TSS	Rectal Smooth Muscle	rectum
19	chr5:96518400-96520000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr5:96518400-96520000	Active TSS	Brain Hippocampus Middle	brain
21	chr5:96518400-96520000	Active TSS	Fetal Kidney	kidney
22	chr5:96518400-96520200	Active TSS	Fetal Brain Female	brain
23	chr5:96519200-96526200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr5:96519400-96520000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr5:96519400-96520000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
26	chr5:96519400-96520000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:96519400-96520000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:96519400-96520000	Flanking Active TSS	Fetal Muscle Trunk	muscle
29	chr5:96519600-96520000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr5:96519600-96520000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr5:96519600-96520000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr5:96519600-96520000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr5:96519600-96520000	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr5:96519600-96520000	Flanking Active TSS	Primary B cells from peripheral blood	blood
35	chr5:96519600-96520000	Flanking Active TSS	Primary T cells from cord blood	blood
36	chr5:96519600-96520000	Flanking Active TSS	Primary hematopoietic stem cells	blood
37	chr5:96519600-96520000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
38	chr5:96519600-96520000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
39	chr5:96519600-96520000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr5:96519600-96520000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr5:96519600-96520000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr5:96519600-96520000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr5:96519600-96520000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr5:96519600-96520000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:96519600-96520000	Flanking Active TSS	Adipose Nuclei	Adipose
46	chr5:96519600-96520000	Flanking Active TSS	Liver	Liver
47	chr5:96519600-96520000	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr5:96519600-96520000	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr5:96519600-96520000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr5:96519600-96520000	Flanking Active TSS	Fetal Brain Male	brain

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