Variant report

Variant	rs1499517
Chromosome Location	chr14:65229006-65229007
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	EP300	chr14:65226747-65231955	SK-N-SH	brain:	n/a	chr14:65229497-65229513 chr14:65231359-65231366 chr14:65228770-65228786 chr14:65231099-65231108
2	NR3C1	chr14:65228666-65229230	A549	lung:	n/a	chr14:65228714-65228721
3	STAT3	chr14:65228740-65229041	MCF10A-Er-Src	breast:	n/a	n/a
4	TCF12	chr14:65228756-65229404	A549	lung:	n/a	chr14:65229381-65229391 chr14:65229172-65229182
5	STAT3	chr14:65228693-65229068	MCF10A-Er-Src	breast:	n/a	n/a
6	REST	chr14:65228455-65229613	A549	lung:	n/a	chr14:65228473-65228481 chr14:65229146-65229159
7	TCF12	chr14:65228254-65229533	ECC-1	luminal epithelium:	n/a	chr14:65228725-65228733 chr14:65229381-65229391 chr14:65229172-65229182 chr14:65228311-65228321
8	POLR2A	chr14:65228121-65230150	K562	blood:	n/a	n/a
9	FOS	chr14:65228695-65229310	MCF10A-Er-Src	breast:	n/a	n/a
10	KAP1	chr14:65228669-65229712	HEK293	kidney:	n/a	n/a
11	ZNF217	chr14:65228937-65229295	MCF-7	breast:	n/a	n/a
12	MXI1	chr14:65228347-65229692	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr14:65228710-65229352	MCF10A-Er-Src	breast:	n/a	n/a
14	ZNF263	chr14:65228550-65229746	HEK293-T-REx	kidney:	n/a	n/a
15	MAX	chr14:65228386-65229907	MCF-7	breast:	n/a	n/a
16	EP300	chr14:65228528-65229319	Hela-S3	cervix:	n/a	chr14:65228770-65228786
17	MAX	chr14:65228436-65229827	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr14:65228324-65229770	Hela-S3	cervix:	n/a	n/a
19	NFIC	chr14:65228548-65229459	SK-N-SH	brain:	n/a	chr14:65229217-65229233 chr14:65229217-65229234 chr14:65229120-65229137
20	RCOR1	chr14:65227974-65229796	IMR90	lung:	n/a	n/a
21	RFX5	chr14:65228388-65229866	Hela-S3	cervix:	n/a	chr14:65229161-65229175
22	MAX	chr14:65228278-65230044	A549	lung:	n/a	n/a
23	MYC	chr14:65228640-65229112	MCF10A-Er-Src	breast:	n/a	n/a
24	RAD21	chr14:65228875-65229303	SK-N-SH_RA	brain:	n/a	chr14:65229182-65229195
25	SIN3AK20	chr14:65228741-65229320	A549	lung:	n/a	n/a
26	TFAP2A	chr14:65228270-65230119	Hela-S3	cervix:	n/a	chr14:65229778-65229793 chr14:65229563-65229578 chr14:65229781-65229795 chr14:65229781-65229795 chr14:65229441-65229452 chr14:65229783-65229795 chr14:65229783-65229794
27	GATA1	chr14:65228761-65229560	PBDE	blood:	n/a	chr14:65229481-65229497
28	SP1	chr14:65228293-65229656	A549	lung:	n/a	chr14:65229056-65229066
29	TBP	chr14:65228393-65229217	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr14:65228900-65229050	AG04450	lung:	n/a	n/a
31	BCL3	chr14:65228416-65229594	A549	lung:	n/a	chr14:65228768-65228781 chr14:65228417-65228425
32	TCF12	chr14:65228155-65229895	A549	lung:	n/a	chr14:65228725-65228733 chr14:65229381-65229391 chr14:65229172-65229182 chr14:65228311-65228321
33	MAFK	chr14:65228792-65229414	IMR90	lung:	n/a	n/a
34	POLR2A	chr14:65228059-65229558	ECC-1	luminal epithelium:	n/a	n/a
35	NR3C1	chr14:65228758-65229400	A549	lung:	n/a	n/a
36	USF1	chr14:65228772-65229627	A549	lung:	n/a	chr14:65229496-65229512
37	EP300	chr14:65228682-65229397	ECC-1	luminal epithelium:	n/a	chr14:65228770-65228786
38	MAX	chr14:65228335-65229820	A549	lung:	n/a	n/a
39	TCF7L2	chr14:65228428-65229682	Hela-S3	cervix:	n/a	n/a
40	RCOR1	chr14:65228955-65229210	K562	blood:	n/a	n/a
41	POLR2A	chr14:65227527-65230282	ECC-1	luminal epithelium:	n/a	n/a
42	JUND	chr14:65228644-65229416	A549	lung:	n/a	n/a
43	RAD21	chr14:65228408-65229337	IMR90	lung:	n/a	chr14:65228771-65228784 chr14:65228769-65228783 chr14:65229182-65229195
44	FOXP2	chr14:65229000-65229293	PFSK-1	brain:	n/a	n/a
45	BCL3	chr14:65228493-65229464	A549	lung:	n/a	chr14:65228768-65228781
46	NFIC	chr14:65228253-65229668	ECC-1	luminal epithelium:	n/a	chr14:65229217-65229233 chr14:65229217-65229234 chr14:65229120-65229137
47	TCF7L2	chr14:65228619-65229276	HCT-116	colon:	n/a	n/a
48	EGR1	chr14:65228947-65229203	K562	blood:	n/a	n/a
49	ZKSCAN1	chr14:65228386-65229691	Hela-S3	cervix:	n/a	chr14:65229561-65229574
50	RAD21	chr14:65226715-65232277	SK-N-SH	brain:	n/a	chr14:65226775-65226787 chr14:65228771-65228784 chr14:65231656-65231675 chr14:65228769-65228783 chr14:65229999-65230012 chr14:65230645-65230664 chr14:65230007-65230020 chr14:65231449-65231463 chr14:65227072-65227091 chr14:65231658-65231670 chr14:65228012-65228025 chr14:65229182-65229195

No.	Distal block	Cell Line	Cell type
1	chr14:65228573..65229471-chr14:65266358..65267017,2	MCF-7	breast:
2	chr14:65195829..65198759-chr14:65228499..65232345,3	MCF-7	breast:
3	chr14:65227919..65230155-chr14:65235739..65238455,3	K562	blood:
4	chr14:65222955..65224467-chr14:65226753..65229376,2	K562	blood:
5	chr14:65228571..65230155-chr14:65235739..65238455,2	K562	blood:
6	chr14:64970824..64972930-chr14:65228597..65230283,2	MCF-7	breast:
7	chr14:65192290..65195649-chr14:65222693..65231374,9	MCF-7	breast:
8	chr14:65168373..65176902-chr14:65220182..65231670,21	MCF-7	breast:
9	chr14:65168335..65178043-chr14:65220677..65234710,31	MCF-7	breast:
10	chr14:65221170..65226335-chr14:65227109..65232798,8	MCF-7	breast:
11	chr14:65228067..65229645-chr14:65348002..65349763,2	K562	blood:
12	chr14:64969302..64971888-chr14:65227488..65230502,4	MCF-7	breast:

Variant related genes	Relation type
SPTB	TF binding region
ENSG00000089775	Chromatin interaction
ENSG00000126822	Chromatin interaction
ENSG00000126804	Chromatin interaction
ENSG00000070182	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs17180385	0.85[ASN][1000 genomes]
rs59914095	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60545775	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs747860	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[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	esv1818582	chr14:65172898-65256685	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1035833	chr14:65176371-65246181	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv1801406	chr14:65193725-65264416	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	11 gene(s)	inside rSNPs	diseases
4	nsv902023	chr14:65200821-65243885	Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv902024	chr14:65200821-65244950	Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65215200-65232400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr14:65219400-65230000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr14:65220600-65232200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr14:65220800-65233000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr14:65221200-65231600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr14:65221200-65231600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr14:65221400-65229800	Enhancers	Pancreas	Pancrea
8	chr14:65221400-65230000	Enhancers	Fetal Intestine Small	intestine
9	chr14:65221400-65231600	Enhancers	Spleen	Spleen
10	chr14:65221400-65232600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr14:65221600-65232400	Enhancers	Fetal Intestine Large	intestine
12	chr14:65221800-65232200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr14:65222000-65229200	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr14:65222200-65229600	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr14:65222200-65231600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr14:65222400-65230000	Enhancers	Stomach Mucosa	stomach
17	chr14:65222600-65231600	Enhancers	Fetal Heart	heart
18	chr14:65223200-65229400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr14:65223200-65229800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr14:65223400-65229800	Enhancers	Left Ventricle	heart
21	chr14:65223400-65230000	Enhancers	Fetal Muscle Trunk	muscle
22	chr14:65223600-65230200	Weak transcription	Primary T cells from cord blood	blood
23	chr14:65223600-65230600	Enhancers	Right Ventricle	heart
24	chr14:65223600-65231600	Enhancers	Ovary	ovary
25	chr14:65223600-65232200	Enhancers	Fetal Stomach	stomach
26	chr14:65224000-65231400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr14:65225200-65229200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr14:65225200-65230800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr14:65225200-65231200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr14:65225400-65229200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr14:65225400-65229600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr14:65226200-65229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr14:65227200-65229400	Bivalent Enhancer	Placenta	Placenta
34	chr14:65227400-65231000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr14:65227400-65231600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr14:65227600-65229400	Enhancers	Rectal Smooth Muscle	rectum
37	chr14:65227600-65229800	Enhancers	Right Atrium	heart
38	chr14:65227600-65231600	Enhancers	Fetal Lung	lung
39	chr14:65227600-65231600	Enhancers	Fetal Thymus	thymus
40	chr14:65227600-65232800	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr14:65227800-65229200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr14:65227800-65229400	Enhancers	Small Intestine	intestine
43	chr14:65227800-65230000	Enhancers	Fetal Muscle Leg	muscle
44	chr14:65227800-65231600	Enhancers	Duodenum Smooth Muscle	Duodenum
45	chr14:65228000-65229200	Enhancers	Colonic Mucosa	Colon
46	chr14:65228000-65229600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr14:65228000-65229800	Enhancers	Fetal Brain Male	brain
48	chr14:65228000-65229800	Enhancers	Gastric	stomach
49	chr14:65228000-65230000	Flanking Active TSS	Hela-S3	cervix
50	chr14:65228000-65231000	Enhancers	Primary hematopoietic stem cells short term culture	blood

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