Variant report

Variant	rs10406924
Chromosome Location	chr19:39929419-39929420
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	EP300	chr19:39929272-39929500	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr19:39929070-39929673	A549	lung:	n/a	chr19:39929392-39929403
3	ATF3	chr19:39929328-39929463	HepG2	liver:	n/a	n/a
4	RCOR1	chr19:39929294-39929519	K562	blood:	n/a	n/a
5	POLR2A	chr19:39886400-39939626	PANC-1	pancreas:	n/a	n/a
6	CEBPB	chr19:39929301-39929523	HepG2	liver:	n/a	chr19:39929392-39929403
7	TEAD4	chr19:39929119-39929614	HepG2	liver:	n/a	n/a
8	CEBPD	chr19:39929209-39929555	HepG2	liver:	n/a	n/a
9	CEBPB	chr19:39929186-39929568	K562	blood:	n/a	chr19:39929392-39929403
10	TEAD4	chr19:39929232-39929530	K562	blood:	n/a	n/a
11	CEBPB	chr19:39929266-39929581	HepG2	liver:	n/a	chr19:39929392-39929403
12	TEAD4	chr19:39929095-39929536	ECC-1	luminal epithelium:	n/a	n/a
13	JUND	chr19:39929282-39929551	HepG2	liver:	n/a	n/a
14	ZNF384	chr19:39929209-39929526	K562	blood:	n/a	n/a
15	TEAD4	chr19:39929213-39929649	K562	blood:	n/a	n/a
16	HDAC2	chr19:39929363-39929498	K562	blood:	n/a	n/a
17	CEBPB	chr19:39929217-39929582	IMR90	lung:	n/a	chr19:39929392-39929403
18	FOS	chr19:39929232-39929558	MCF10A-Er-Src	breast:	n/a	n/a
19	TEAD4	chr19:39929274-39929476	HepG2	liver:	n/a	n/a
20	TEAD4	chr19:39929266-39929517	H1-hESC	embryonic stem cell:	n/a	n/a
21	CEBPB	chr19:39929143-39929566	ECC-1	luminal epithelium:	n/a	chr19:39929392-39929403
22	CEBPB	chr19:39929204-39929547	A549	lung:	n/a	chr19:39929392-39929403
23	CEBPB	chr19:39929261-39929555	K562	blood:	n/a	chr19:39929392-39929403
24	POLR2A	chr19:39886449-39939600	PANC-1	pancreas:	n/a	n/a
25	ARID3A	chr19:39929275-39929517	HepG2	liver:	n/a	n/a
26	CEBPB	chr19:39929208-39929579	Hela-S3	cervix:	n/a	chr19:39929392-39929403
27	CEBPB	chr19:39929259-39929528	K562	blood:	n/a	chr19:39929392-39929403
28	FOS	chr19:39929265-39929563	MCF10A-Er-Src	breast:	n/a	n/a
29	CEBPB	chr19:39929251-39929567	A549	lung:	n/a	chr19:39929392-39929403
30	FOS	chr19:39929267-39929557	MCF10A-Er-Src	breast:	n/a	n/a
31	CEBPB	chr19:39929271-39929560	H1-hESC	embryonic stem cell:	n/a	chr19:39929392-39929403
32	CEBPD	chr19:39929239-39929534	HepG2	liver:	n/a	n/a
33	CEBPB	chr19:39929222-39929529	ECC-1	luminal epithelium:	n/a	chr19:39929392-39929403
34	CEBPB	chr19:39929221-39929563	HepG2	liver:	n/a	chr19:39929392-39929403
35	TEAD4	chr19:39929211-39929545	ECC-1	luminal epithelium:	n/a	n/a
36	CEBPB	chr19:39929175-39929505	MCF-7	breast:	n/a	chr19:39929392-39929403
37	CEBPB	chr19:39929222-39929510	HepG2	liver:	n/a	chr19:39929392-39929403
38	ATF3	chr19:39929278-39929517	K562	blood:	n/a	n/a
39	JUND	chr19:39929343-39929433	K562	blood:	n/a	n/a
40	FOS	chr19:39929254-39929525	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
SUPT5H	TF binding region
RPS16	TF binding region
ENSG00000213922	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1865090	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1865093	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802032	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4803238	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv870133	chr19:39822160-39938468	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv911685	chr19:39888449-39948779	Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	222 gene(s)	inside rSNPs	diseases
3	nsv911689	chr19:39903088-40021759	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
5	nsv523856	chr19:39913558-39997472	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
6	esv1791966	chr19:39921479-39954931	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10406924	RPS16	cis	Heart Left Ventricle	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39926600-39935200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:39927400-39929800	Enhancers	Placenta	Placenta
3	chr19:39927400-39930200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:39927400-39930400	Weak transcription	K562	blood
5	chr19:39927400-39930800	Weak transcription	Brain Angular Gyrus	brain
6	chr19:39927400-39935200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:39927400-39935200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:39927400-39935200	Weak transcription	Gastric	stomach
9	chr19:39927400-39935200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr19:39927600-39930200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr19:39927600-39930200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr19:39927600-39930600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr19:39927600-39930600	Weak transcription	GM12878-XiMat	blood
14	chr19:39927600-39930800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr19:39927600-39930800	Weak transcription	Brain Hippocampus Middle	brain
16	chr19:39927600-39930800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr19:39927600-39930800	Weak transcription	Fetal Heart	heart
18	chr19:39927600-39931000	Weak transcription	Primary B cells from cord blood	blood
19	chr19:39927600-39931000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr19:39927600-39931000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:39927600-39931000	Weak transcription	Liver	Liver
22	chr19:39927600-39931000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr19:39927600-39931000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr19:39927600-39932000	Enhancers	A549	lung
25	chr19:39927600-39934800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr19:39927600-39935000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr19:39927600-39935000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:39927600-39935000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:39927600-39935000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr19:39927600-39935000	Weak transcription	HMEC	breast
31	chr19:39927600-39935200	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr19:39927600-39935200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr19:39927600-39935200	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr19:39927600-39935200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr19:39927600-39935200	Weak transcription	Brain Anterior Caudate	brain
36	chr19:39927600-39935200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr19:39927600-39935200	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr19:39927600-39935200	Weak transcription	Fetal Kidney	kidney
39	chr19:39927600-39935200	Weak transcription	HSMMtube	muscle
40	chr19:39927600-39935200	Weak transcription	NHLF	lung
41	chr19:39927800-39931000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:39927800-39931000	Weak transcription	Dnd41	blood
43	chr19:39927800-39931200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:39928400-39930000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr19:39928600-39930800	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr19:39928600-39935000	Weak transcription	Fetal Intestine Small	intestine
47	chr19:39928800-39929600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr19:39928800-39929600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:39928800-39930600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr19:39929000-39930800	Weak transcription	Hela-S3	cervix

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