Variant report

Variant	rs12590407
Chromosome Location	chr14:24835115-24835116
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	CTCF	chr14:24834873-24835149	GM10248	blood:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
2	NFIC	chr14:24834906-24835642	ECC-1	luminal epithelium:	n/a	n/a
3	CTCF	chr14:24834848-24835216	GM12891	blood:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
4	SIN3AK20	chr14:24834707-24837100	MCF-7	breast:	n/a	n/a
5	NR2F2	chr14:24834817-24837037	MCF-7	breast:	n/a	n/a
6	CTCF	chr14:24834743-24835160	A549	lung:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
7	POLR2A	chr14:24834943-24836204	MCF-7	breast:	n/a	n/a
8	RAD21	chr14:24834810-24835315	H1-hESC	embryonic stem cell:	n/a	chr14:24835243-24835255 chr14:24835037-24835056 chr14:24835042-24835052 chr14:24835042-24835054
9	RUNX3	chr14:24834703-24835306	GM12878	blood:	n/a	n/a
10	SP1	chr14:24834644-24837454	HCT-116	colon:	n/a	chr14:24836464-24836478 chr14:24835192-24835204 chr14:24835866-24835875 chr14:24836438-24836452 chr14:24837289-24837303 chr14:24837103-24837117 chr14:24835021-24835030 chr14:24835193-24835203 chr14:24836442-24836451 chr14:24835368-24835382 chr14:24835866-24835875 chr14:24835192-24835204 chr14:24837056-24837063 chr14:24836441-24836453 chr14:24836443-24836452 chr14:24835193-24835207 chr14:24835193-24835202 chr14:24835540-24835549 chr14:24835865-24835877 chr14:24836442-24836452 chr14:24835867-24835876 chr14:24835541-24835550 chr14:24837317-24837338 chr14:24835194-24835203 chr14:24836441-24836453
11	RAD21	chr14:24834757-24835251	H1-hESC	embryonic stem cell:	n/a	chr14:24835037-24835056 chr14:24835042-24835052 chr14:24835042-24835054
12	PBX3	chr14:24834836-24837421	SK-N-SH	brain:	n/a	chr14:24837319-24837328 chr14:24835856-24835876
13	RAD21	chr14:24834611-24835490	HCT-116	colon:	n/a	chr14:24835243-24835255 chr14:24835037-24835056 chr14:24835042-24835052 chr14:24835042-24835054
14	CTCF	chr14:24834869-24835148	SK-N-SH_RA	brain:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
15	CTCF	chr14:24834827-24835202	GM12878	blood:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
16	MBD4	chr14:24834709-24835495	HepG2	liver:	n/a	n/a
17	CTCF	chr14:24834841-24835167	Pancreas_OC	pancreas:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
18	CTCF	chr14:24834815-24835169	HUVEC	blood vessel:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
19	GATA3	chr14:24834893-24835139	T-47D	breast:	n/a	n/a
20	CHD1	chr14:24834050-24838822	IMR90	lung:	n/a	chr14:24835865-24835875
21	POLR2A	chr14:24834712-24836862	HUVEC	blood vessel:	n/a	n/a
22	CTCF	chr14:24834837-24835115	K562	blood:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
23	CTCF	chr14:24834844-24835210	T-47D	breast:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
24	TCF7L2	chr14:24835103-24836269	Hela-S3	cervix:	n/a	chr14:24835466-24835480 chr14:24835467-24835481 chr14:24835468-24835478 chr14:24835470-24835479 chr14:24835466-24835482 chr14:24835466-24835482
25	RAD21	chr14:24834705-24835357	ECC-1	luminal epithelium:	n/a	chr14:24835243-24835255 chr14:24835037-24835056 chr14:24835042-24835052 chr14:24835042-24835054
26	E2F4	chr14:24834798-24835474	MCF10A-Er-Src	breast:	n/a	chr14:24835194-24835203
27	CTCF	chr14:24834775-24835245	T-47D	breast:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
28	CTCF	chr14:24834861-24835190	Fibrobl	skin:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
29	RAD21	chr14:24834764-24835185	GM12878	blood:	n/a	chr14:24835037-24835056 chr14:24835042-24835052 chr14:24835042-24835054
30	CTCF	chr14:24834499-24835582	HCT-116	colon:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
31	MAZ	chr14:24834831-24835249	GM12878	blood:	n/a	chr14:24835199-24835209
32	GATA3	chr14:24834707-24836970	MCF-7	breast:	n/a	n/a
33	POLR2A	chr14:24834867-24838188	HUVEC	blood vessel:	n/a	n/a
34	CTCF	chr14:24834808-24835157	SK-N-SH_RA	brain:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
35	ZBTB7A	chr14:24834842-24835202	HepG2	liver:	n/a	n/a
36	CTCF	chr14:24834848-24835188	MCF-7	breast:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
37	CTCF	chr14:24834840-24835130	HCM	heart:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
38	TEAD4	chr14:24834832-24835175	H1-hESC	embryonic stem cell:	n/a	n/a
39	CTCF	chr14:24834521-24835464	HepG2	liver:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
40	CTCF	chr14:24834810-24835127	ECC-1	luminal epithelium:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
41	POLR2A	chr14:24834945-24836167	ProgFib	skin:	n/a	n/a
42	RAD21	chr14:24834735-24835252	ECC-1	luminal epithelium:	n/a	chr14:24835037-24835056 chr14:24835042-24835052 chr14:24835042-24835054
43	POLR2A	chr14:24834737-24836856	SK-N-SH	brain:	n/a	n/a
44	CTCF	chr14:24834865-24835168	ProgFib	skin:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
45	ZNF143	chr14:24834815-24835219	H1-hESC	embryonic stem cell:	n/a	n/a
46	CTCF	chr14:24834762-24835237	GM12878	blood:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
47	CTCF	chr14:24834760-24835249	K562	blood:	n/a	chr14:24835036-24835054 chr14:24835039-24835052
48	CEBPB	chr14:24834934-24835528	IMR90	lung:	n/a	n/a
49	POLR2A	chr14:24834888-24837326	Raji	blood:	n/a	n/a
50	NFIC	chr14:24834829-24835261	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr14:24835104-24835154	HPAEpiC	pulmonary alveolar:	n/a
2	chr14:24835104-24835154	HL-60	blood:	n/a
3	chr14:24835104-24835154	HRE	kidney:	n/a
4	chr14:24835104-24835154	HEK293	kidney:	embryo
5	chr14:24835104-24835154	CMK	blood:	n/a
6	chr14:24835104-24835154	AG09309	skin:	n/a
7	chr14:24835104-24835154	HCM	heart:	n/a
8	chr14:24835104-24835154	NT2-D1	testis:	n/a
9	chr14:24835104-24835154	HNPCEpiC	eye:	n/a
10	chr14:24835104-24835154	ProgFib	skin:	n/a
11	chr14:24835104-24835154	BJ	skin:	n/a
12	chr14:24835104-24835154	SK-N-MC	brain:	n/a
13	chr14:24835104-24835154	HAEpiC	amniotic membrane:	n/a
14	chr14:24835104-24835154	AG04449	skin:	fetal
15	chr14:24835104-24835154	GM12892	blood:	n/a
16	chr14:24835104-24835154	A549	lung:	n/a
17	chr14:24835104-24835154	K562	blood:	n/a
18	chr14:24835104-24835154	Caco-2	colon:	n/a
19	chr14:24835104-24835154	SK-N-SH	brain:	n/a
20	chr14:24835104-24835154	GM12891	blood:	n/a
21	chr14:24835104-24835154	Hepatocyte	liver:	n/a
22	chr14:24835104-24835154	ECC-1	luminal epithelium:	n/a
23	chr14:24835104-24835154	BE2_C	brain:	n/a
24	chr14:24835104-24835154	AG10803	skin:	n/a
25	chr14:24835104-24835154	AG04450	lung:	fetal
26	chr14:24835104-24835154	SKMC	muscle:	n/a
27	chr14:24835104-24835154	PFSK-1	brain:	n/a
28	chr14:24835104-24835154	HCT-116	colon:	n/a
29	chr14:24835104-24835154	NB4	blood:	n/a
30	chr14:24835104-24835154	HEEpiC	esophagus:	n/a
31	chr14:24835104-24835154	SAEC	small airway:	n/a
32	chr14:24835104-24835154	Hela-S3	cervix:	n/a
33	chr14:24835104-24835154	IMR90	lung:	fetal
34	chr14:24835104-24835154	HMEC	breast:	n/a
35	chr14:24835104-24835154	PrEC	prostate:	n/a
36	chr14:24835104-24835154	HIPEpiC	eye:	n/a
37	chr14:24835104-24835154	HCF	heart:	n/a
38	chr14:24835104-24835154	Jurkat	blood:	n/a
39	chr14:24835104-24835154	PANC-1	pancreas:	n/a
40	chr14:24835104-24835154	GM12878	blood:	n/a
41	chr14:24835104-24835154	SK-N-SH_RA	brain:	n/a
42	chr14:24835104-24835154	ovcar-3	ovarian:	n/a
43	chr14:24835104-24835154	MCF-7	breast:	n/a
44	chr14:24835104-24835154	NH-A	brain:	n/a
45	chr14:24835104-24835154	U87	brain:	n/a
46	chr14:24835104-24835154	NHBE	bronchial:	n/a
47	chr14:24835104-24835154	NHDF-neo	bronchial:	n/a
48	chr14:24835104-24835154	GM06990	blood:	n/a
49	chr14:24835104-24835154	T-47D	breast:	n/a
50	chr14:24835104-24835154	HCPEpiC	choroid plexus:	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:24627394..24630112-chr14:24833031..24835825,2	K562	blood:
2	chr14:24833553..24839988-chr14:24894553..24902357,9	K562	blood:
3	chr14:24827418..24850855-chr14:24894884..24913772,127	MCF-7	breast:
4	chr14:24834361..24836035-chr14:24881010..24881990,12	MCF-7	breast:
5	chr14:24796879..24804920-chr14:24831628..24840088,12	MCF-7	breast:
6	chr14:24816528..24849574-chr14:24893305..24914155,145	MCF-7	breast:
7	chr14:24834498..24835762-chr14:24880980..24882037,25	MCF-7	breast:
8	chr14:24833867..24840783-chr14:24879585..24886299,12	MCF-7	breast:
9	chr14:24831849..24834970-chr14:24835074..24838209,3	K562	blood:
10	chr14:24833707..24839988-chr14:24896546..24902736,10	K562	blood:
11	chr14:24710306..24713162-chr14:24834355..24837181,3	MCF-7	breast:
12	chr14:24801497..24802367-chr14:24834548..24835170,2	MCF-7	breast:
13	chr14:24834934..24835798-chr14:24844850..24845592,2	MCF-7	breast:
14	chr14:24834239..24835761-chr14:24900242..24902851,45	MCF-7	breast:
15	chr14:24805754..24808104-chr14:24833773..24836418,2	MCF-7	breast:
16	chr14:24834749..24836813-chr14:24843858..24845467,2	K562	blood:
17	chr14:24801495..24803055-chr14:24833652..24836395,3	MCF-7	breast:
18	chr14:24834871..24836574-chr14:24881595..24883605,2	MCF-7	breast:

Variant related genes	Relation type
NFATC4	TF binding region
NFATC4	CpG island
ENSG00000129467	Chromatin interaction
ENSG00000258973	Chromatin interaction
ENSG00000100968	Chromatin interaction
ENSG00000129465	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000199804	Chromatin interaction
ENSG00000205978	Chromatin interaction
ENSG00000100445	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000092098	Chromatin interaction
ENSG00000139899	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1950500	1.00[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2144490	0.92[YRI][hapmap]
rs2332327	0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription 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	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12590407	EDDM3A	cis	parietal	SCAN
rs12590407	ADCY4	cis	cerebellum	SCAN
rs12590407	TGM1	cis	cerebellum	SCAN
rs12590407	NFATC4	cis	cerebellum	SCAN
rs12590407	CHMP4A	cis	cerebellum	SCAN
rs12590407	OSGEP	cis	parietal	SCAN
rs12590407	NGDN	cis	parietal	SCAN
rs12590407	DHRS1	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24832200-24835200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:24834200-24835200	Enhancers	Placenta	Placenta
3	chr14:24834200-24835200	Enhancers	Stomach Mucosa	stomach
4	chr14:24834200-24835200	Enhancers	HMEC	breast
5	chr14:24834200-24835600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr14:24834200-24835600	Flanking Active TSS	NHDF-Ad	bronchial
7	chr14:24834400-24835200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr14:24834400-24835200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
9	chr14:24834400-24835200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr14:24834400-24835200	Enhancers	Brain Substantia Nigra	brain
11	chr14:24834400-24835200	Enhancers	Duodenum Mucosa	Duodenum
12	chr14:24834400-24835200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
13	chr14:24834400-24835200	Enhancers	HSMM	muscle
14	chr14:24834400-24835400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr14:24834400-24835400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr14:24834400-24835800	Flanking Active TSS	Osteobl	bone
17	chr14:24834400-24836200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
18	chr14:24834400-24836400	Enhancers	HSMMtube	muscle
19	chr14:24834400-24836600	Enhancers	Fetal Heart	heart
20	chr14:24834600-24835200	Enhancers	Primary B cells from cord blood	blood
21	chr14:24834600-24835200	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
22	chr14:24834600-24835200	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
23	chr14:24834600-24835200	Enhancers	Liver	Liver
24	chr14:24834600-24835200	Enhancers	Fetal Stomach	stomach
25	chr14:24834600-24835200	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr14:24834600-24835200	Enhancers	GM12878-XiMat	blood
27	chr14:24834600-24835400	Enhancers	Brain Angular Gyrus	brain
28	chr14:24834600-24835400	Flanking Active TSS	NHLF	lung
29	chr14:24834600-24835600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
30	chr14:24834600-24835600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr14:24834600-24835600	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr14:24834600-24835600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr14:24834600-24835600	Flanking Active TSS	Fetal Lung	lung
34	chr14:24834600-24835800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr14:24834600-24836000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
36	chr14:24834800-24835200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
37	chr14:24834800-24835200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr14:24834800-24835200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr14:24834800-24835200	Enhancers	Lung	lung
40	chr14:24834800-24835400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
41	chr14:24834800-24835400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr14:24834800-24835400	Flanking Active TSS	NH-A	brain
43	chr14:24834800-24835600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
44	chr14:24834800-24835600	Enhancers	Primary hematopoietic stem cells	blood
45	chr14:24834800-24835600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr14:24834800-24835800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
47	chr14:24834800-24835800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
48	chr14:24834800-24836600	Bivalent Enhancer	Fetal Brain Male	brain
49	chr14:24834800-24837200	Flanking Active TSS	HUVEC	blood vessel
50	chr14:24834800-24837200	Flanking Active TSS	NHEK	skin

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