Variant report

Variant	rs12609014
Chromosome Location	chr19:40725754-40725755
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	SMC3	chr19:40725580-40726191	Hela-S3	cervix:	n/a	n/a
2	FOSL2	chr19:40725204-40726345	A549	lung:	n/a	chr19:40725918-40725929 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725920-40725928 chr19:40725920-40725928
3	KAP1	chr19:40725562-40726014	U2OS	brain:	n/a	n/a
4	FOS	chr19:40725557-40726167	MCF10A-Er-Src	breast:	n/a	chr19:40725918-40725929 chr19:40725947-40725958 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725918-40725929 chr19:40725920-40725928 chr19:40725920-40725928
5	EP300	chr19:40725705-40726098	K562	blood:	n/a	chr19:40725919-40725928
6	RCOR1	chr19:40725611-40726099	K562	blood:	n/a	n/a
7	POLR2A	chr19:40725328-40726029	Hela-S3	cervix:	n/a	n/a
8	JUN	chr19:40725573-40726102	K562	blood:	n/a	chr19:40725918-40725929 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725920-40725928 chr19:40725920-40725928
9	FOSL2	chr19:40725365-40726224	SK-N-SH	brain:	n/a	chr19:40725918-40725929 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725920-40725928 chr19:40725920-40725928
10	EGR1	chr19:40725560-40726218	K562	blood:	n/a	n/a
11	NFIC	chr19:40725451-40726012	ECC-1	luminal epithelium:	n/a	n/a
12	TCF7L2	chr19:40725346-40726207	HCT-116	colon:	n/a	n/a
13	JUND	chr19:40725523-40726185	K562	blood:	n/a	chr19:40725947-40725958 chr19:40725918-40725929 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725920-40725928 chr19:40725920-40725928
14	MYC	chr19:40725655-40726076	MCF10A-Er-Src	breast:	n/a	chr19:40725924-40725933
15	MYC	chr19:40725633-40725820	K562	blood:	n/a	n/a
16	MAX	chr19:40725557-40726021	SK-N-SH	brain:	n/a	chr19:40725924-40725933
17	JUND	chr19:40725531-40726106	Hela-S3	cervix:	n/a	chr19:40725947-40725958 chr19:40725918-40725929 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725920-40725928 chr19:40725920-40725928
18	USF1	chr19:40725710-40726210	SK-N-SH_RA	brain:	n/a	chr19:40725923-40725934
19	POLR2A	chr19:40725422-40726296	HCT-116	colon:	n/a	n/a
20	MAX	chr19:40725148-40726431	A549	lung:	n/a	chr19:40725924-40725933
21	POLR2A	chr19:40725464-40726030	U87	brain:	n/a	n/a
22	TAF1	chr19:40725446-40726306	PFSK-1	brain:	n/a	n/a
23	JUND	chr19:40725327-40726683	HCT-116	colon:	n/a	chr19:40725947-40725958 chr19:40725918-40725929 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725920-40725928 chr19:40725920-40725928
24	FOS	chr19:40725510-40726114	MCF10A-Er-Src	breast:	n/a	chr19:40725918-40725929 chr19:40725947-40725958 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725918-40725929 chr19:40725920-40725928 chr19:40725920-40725928
25	USF1	chr19:40725603-40726335	SK-N-SH	brain:	n/a	chr19:40725923-40725934
26	FOS	chr19:40725526-40726181	MCF10A-Er-Src	breast:	n/a	chr19:40725918-40725929 chr19:40725947-40725958 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725918-40725929 chr19:40725920-40725928 chr19:40725920-40725928
27	POLR2A	chr19:40725616-40726057	SK-N-SH	brain:	n/a	n/a
28	REST	chr19:40725506-40726209	PFSK-1	brain:	n/a	chr19:40726153-40726161
29	E2F6	chr19:40725607-40725873	K562	blood:	n/a	n/a
30	E2F4	chr19:40725549-40726086	MCF10A-Er-Src	breast:	n/a	n/a
31	TCF7L2	chr19:40725609-40726022	PANC-1	pancreas:	n/a	n/a
32	USF1	chr19:40725431-40726428	HCT-116	colon:	n/a	chr19:40725923-40725934
33	ARID3A	chr19:40725690-40725982	K562	blood:	n/a	n/a
34	USF1	chr19:40725721-40726114	A549	lung:	n/a	chr19:40725923-40725934
35	USF1	chr19:40725510-40726164	A549	lung:	n/a	chr19:40725923-40725934
36	ZNF263	chr19:40725405-40726271	HEK293-T-REx	kidney:	n/a	chr19:40726016-40726025 chr19:40725707-40725728 chr19:40725747-40725768
37	JUN	chr19:40725543-40726173	K562	blood:	n/a	chr19:40725918-40725929 chr19:40725916-40725927 chr19:40725921-40725928 chr19:40725920-40725928 chr19:40725920-40725928
38	POLR2A	chr19:40725510-40725978	HCT-116	colon:	n/a	n/a
39	USF2	chr19:40725515-40726289	Hela-S3	cervix:	n/a	chr19:40725923-40725934
40	REST	chr19:40721682-40727491	PANC-1	pancreas:	n/a	chr19:40721931-40721944 chr19:40726153-40726161
41	ZNF384	chr19:40725529-40725858	K562	blood:	n/a	n/a
42	REST	chr19:40725558-40725763	K562	blood:	n/a	n/a
43	REST	chr19:40725278-40726083	A549	lung:	n/a	n/a
44	E2F6	chr19:40725337-40726251	A549	lung:	n/a	n/a
45	EP300	chr19:40725710-40726088	Hela-S3	cervix:	n/a	chr19:40725919-40725928
46	MAX	chr19:40725377-40726317	A549	lung:	n/a	chr19:40725924-40725933
47	GTF2F1	chr19:40725560-40726039	Hela-S3	cervix:	n/a	n/a
48	USF1	chr19:40725603-40726204	SK-N-SH_RA	brain:	n/a	chr19:40725923-40725934
49	NFIC	chr19:40725421-40726194	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr19:40725491-40726030	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40724342..40727794-chr19:40739430..40743149,3	K562	blood:
2	chr19:40697008..40699890-chr19:40723055..40726049,3	MCF-7	breast:

Variant related genes	Relation type
TTC9B	TF binding region
ENSG00000130758	Chromatin interaction
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10423675	0.85[ASN][1000 genomes]
rs2304186	0.85[ASN][1000 genomes]
rs34894858	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35562135	0.80[ASN][1000 genomes]
rs3746006	0.81[ASN][1000 genomes]
rs4803317	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55710849	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67322193	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs892117	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	nsv911701	chr19:40695598-40728417	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv911702	chr19:40697061-40731371	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv911703	chr19:40711333-40730279	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv911704	chr19:40716652-40730279	Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
9	nsv911705	chr19:40716652-40731371	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
10	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12609014	MAP3K10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40711200-40731800	Weak transcription	Right Atrium	heart
2	chr19:40723800-40729000	Weak transcription	Gastric	stomach
3	chr19:40724200-40729000	Weak transcription	Pancreas	Pancrea
4	chr19:40724600-40726000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr19:40725200-40725800	Bivalent Enhancer	Fetal Intestine Large	intestine
6	chr19:40725200-40725800	Bivalent Enhancer	Fetal Intestine Small	intestine
7	chr19:40725200-40726200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr19:40725200-40726400	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr19:40725200-40726400	Enhancers	K562	blood
10	chr19:40725400-40725800	Bivalent Enhancer	Stomach Mucosa	stomach
11	chr19:40725400-40726000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr19:40725400-40726000	Active TSS	HSMMtube	muscle
13	chr19:40725400-40726200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr19:40725400-40726200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:40725400-40726200	Flanking Active TSS	A549	lung
16	chr19:40725400-40726200	Flanking Active TSS	Hela-S3	cervix
17	chr19:40725400-40727000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:40725600-40725800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:40725600-40725800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr19:40725600-40725800	Enhancers	Brain Angular Gyrus	brain
21	chr19:40725600-40725800	Bivalent Enhancer	Brain Germinal Matrix	brain
22	chr19:40725600-40726000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr19:40725600-40726000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:40725600-40726000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr19:40725600-40726000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
26	chr19:40725600-40726000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:40725600-40726000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr19:40725600-40726000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr19:40725600-40726000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr19:40725600-40726000	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
31	chr19:40725600-40726000	Flanking Active TSS	HMEC	breast
32	chr19:40725600-40726000	Flanking Active TSS	HSMM	muscle
33	chr19:40725600-40726000	Flanking Active TSS	HUVEC	blood vessel
34	chr19:40725600-40726000	Flanking Active TSS	NH-A	brain
35	chr19:40725600-40726000	Flanking Active TSS	NHDF-Ad	bronchial
36	chr19:40725600-40726000	Flanking Active TSS	NHEK	skin
37	chr19:40725600-40726000	Flanking Active TSS	NHLF	lung
38	chr19:40725600-40726000	Flanking Active TSS	Osteobl	bone
39	chr19:40725600-40726400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland

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