Variant report

Variant	rs1476609
Chromosome Location	chr14:71222065-71222066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:74)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:74 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR3C1	chr14:71221716-71222193	ECC-1	luminal epithelium:	n/a	n/a
2	CTCF	chr14:71222000-71222150	NHEK	skin:	n/a	n/a
3	FOSL1	chr14:71221557-71222275	HCT-116	colon:	n/a	n/a
4	EP300	chr14:71221629-71222073	T-47D	breast:	n/a	n/a
5	EP300	chr14:71221483-71222314	A549	lung:	n/a	n/a
6	TCF12	chr14:71221412-71222583	ECC-1	luminal epithelium:	n/a	n/a
7	FOS	chr14:71221702-71222233	MCF10A-Er-Src	breast:	n/a	n/a
8	STAT3	chr14:71221786-71222098	MCF10A-Er-Src	breast:	n/a	n/a
9	SP1	chr14:71221445-71222268	A549	lung:	n/a	n/a
10	RAD21	chr14:71221632-71222294	ECC-1	luminal epithelium:	n/a	n/a
11	NFIC	chr14:71221412-71222422	ECC-1	luminal epithelium:	n/a	n/a
12	JUND	chr14:71221720-71222303	Hela-S3	cervix:	n/a	chr14:71221915-71221926
13	STAT3	chr14:71221974-71222117	MCF10A-Er-Src	breast:	n/a	n/a
14	CHD2	chr14:71221676-71222168	Hela-S3	cervix:	n/a	n/a
15	TEAD4	chr14:71221539-71222361	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr14:71221524-71222311	ECC-1	luminal epithelium:	n/a	n/a
17	RCOR1	chr14:71221715-71222172	Hela-S3	cervix:	n/a	n/a
18	GATA3	chr14:71221621-71222208	T-47D	breast:	n/a	n/a
19	TCF12	chr14:71221572-71222216	SK-N-SH	brain:	n/a	n/a
20	CEBPB	chr14:71221648-71222233	Hela-S3	cervix:	n/a	n/a
21	JUND	chr14:71221705-71222198	A549	lung:	n/a	chr14:71221915-71221926
22	FOSL1	chr14:71221648-71222260	HCT-116	colon:	n/a	n/a
23	MAX	chr14:71221567-71222325	A549	lung:	n/a	n/a
24	POLR2A	chr14:71221770-71222146	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr14:71222020-71222170	WERI-Rb-1	eye:	n/a	n/a
26	JUND	chr14:71221648-71222425	HCT-116	colon:	n/a	chr14:71221915-71221926
27	USF1	chr14:71221641-71222377	ECC-1	luminal epithelium:	n/a	n/a
28	EP300	chr14:71221531-71222162	T-47D	breast:	n/a	n/a
29	NR3C1	chr14:71221597-71222287	A549	lung:	n/a	n/a
30	JUND	chr14:71221529-71222234	HCT-116	colon:	n/a	chr14:71221915-71221926
31	ESR1	chr14:71221652-71222246	ECC-1	luminal epithelium:	n/a	n/a
32	TCF12	chr14:71221691-71222122	A549	lung:	n/a	n/a
33	TCF12	chr14:71221491-71222379	ECC-1	luminal epithelium:	n/a	n/a
34	STAT3	chr14:71221755-71222134	MCF10A-Er-Src	breast:	n/a	n/a
35	FOSL2	chr14:71221580-71222232	A549	lung:	n/a	n/a
36	NR3C1	chr14:71221782-71222141	A549	lung:	n/a	n/a
37	SP1	chr14:71221591-71222263	A549	lung:	n/a	n/a
38	TEAD4	chr14:71221635-71222175	A549	lung:	n/a	n/a
39	CTCF	chr14:71221920-71222070	HRE	kidney:	n/a	n/a
40	RAD21	chr14:71221692-71222263	Hela-S3	cervix:	n/a	n/a
41	CTCF	chr14:71221960-71222110	Caco-2	colon:	n/a	n/a
42	MAX	chr14:71221520-71222851	ECC-1	luminal epithelium:	n/a	n/a
43	TCF12	chr14:71221496-71222267	A549	lung:	n/a	n/a
44	TCF12	chr14:71221493-71222168	SK-N-SH	brain:	n/a	n/a
45	USF2	chr14:71221589-71222262	Hela-S3	cervix:	n/a	n/a
46	FOSL2	chr14:71221641-71222192	MCF-7	breast:	n/a	n/a
47	SMC3	chr14:71221682-71222214	Hela-S3	cervix:	n/a	n/a
48	NR3C1	chr14:71221709-71222198	A549	lung:	n/a	n/a
49	CTCF	chr14:71222040-71222190	HRE	kidney:	n/a	n/a
50	JUND	chr14:71221581-71222265	T-47D	breast:	n/a	chr14:71221915-71221926

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:71221751..71222316-chr14:71284453..71284972,2	MCF-7	breast:
2	chr14:71221250..71224192-chr14:71276370..71280201,4	MCF-7	breast:
3	chr14:71218602..71225147-chr14:71276029..71280278,8	MCF-7	breast:
4	chr14:71221857..71224156-chr14:71229104..71232104,3	MCF-7	breast:

No data

Variant related genes	Relation type
MAP3K9	TF binding region
ENSG00000259153	Chromatin interaction
ENSG00000006432	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1034769	1.00[CHB][hapmap];0.90[CHD][hapmap];0.92[JPT][hapmap];0.94[ASN][1000 genomes]
rs10873241	0.99[ASN][1000 genomes]
rs10873242	0.87[ASN][1000 genomes]
rs12589737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12879569	0.87[GIH][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs2023955	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2107665	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2107666	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2332455	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2332458	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3814872	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4899368	0.92[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4899369	0.94[ASN][1000 genomes]
rs4902844	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4902852	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4902863	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs6573980	0.99[ASN][1000 genomes]
rs7140653	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7152516	0.91[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs7155910	0.91[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap]
rs8007131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs8011047	0.91[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs8011507	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8018294	0.99[ASN][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	nsv1039460	chr14:71176898-71371125	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	nsv1041980	chr14:71196358-71767339	Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv542125	chr14:71196358-71767339	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1035416	chr14:71212882-71623271	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
5	nsv542126	chr14:71212882-71623271	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1476609	MAP3K9	cis	cerebellum	SCAN
rs1476609	DPF3	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:71197000-71228800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr14:71198400-71223400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr14:71200600-71224200	Weak transcription	Spleen	Spleen
4	chr14:71201200-71228000	Weak transcription	Colonic Mucosa	Colon
5	chr14:71204800-71229400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr14:71206800-71231600	Weak transcription	Brain Anterior Caudate	brain
7	chr14:71209200-71229400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr14:71209400-71238200	Weak transcription	Fetal Stomach	stomach
9	chr14:71209400-71238400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr14:71209400-71238400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr14:71209600-71229000	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr14:71212000-71238200	Weak transcription	Fetal Intestine Small	intestine
13	chr14:71215600-71227000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:71215600-71227400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr14:71215800-71227000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr14:71215800-71232200	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr14:71216200-71226800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr14:71216400-71238200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr14:71216600-71222200	Weak transcription	Primary T cells from cord blood	blood
20	chr14:71216600-71224600	Weak transcription	Placenta	Placenta
21	chr14:71216600-71245800	Weak transcription	Brain Germinal Matrix	brain
22	chr14:71216800-71225600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr14:71216800-71226400	Weak transcription	Duodenum Mucosa	Duodenum
24	chr14:71216800-71238400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr14:71219000-71223600	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr14:71219200-71222400	Enhancers	Stomach Mucosa	stomach
27	chr14:71220200-71222200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr14:71220200-71229000	Weak transcription	Brain Angular Gyrus	brain
29	chr14:71220600-71222200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr14:71220600-71231400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr14:71220600-71238600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr14:71220800-71222200	Enhancers	HepG2	liver
33	chr14:71220800-71227600	Weak transcription	Lung	lung
34	chr14:71220800-71240400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr14:71220800-71266400	Weak transcription	Fetal Intestine Large	intestine
36	chr14:71221000-71237600	Weak transcription	Fetal Kidney	kidney
37	chr14:71221400-71222200	Enhancers	Pancreas	Pancrea
38	chr14:71221400-71223400	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr14:71221400-71223600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr14:71221600-71222200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr14:71221600-71222200	Genic enhancers	Esophagus	oesophagus
42	chr14:71221600-71222200	Enhancers	Left Ventricle	heart
43	chr14:71221600-71222400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr14:71221600-71222400	Enhancers	Fetal Heart	heart
45	chr14:71221600-71222400	Enhancers	Fetal Lung	lung
46	chr14:71221600-71222400	Enhancers	HSMM	muscle
47	chr14:71221600-71222600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr14:71221600-71222600	Flanking Active TSS	A549	lung
49	chr14:71221600-71222600	Enhancers	Hela-S3	cervix
50	chr14:71221600-71223000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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