Variant report

Variant	rs1256542
Chromosome Location	chr14:65769417-65769418
allele	A/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	CEBPB	chr14:65769397-65769633	ECC-1	luminal epithelium:	n/a	n/a
2	TCF12	chr14:65769038-65769809	ECC-1	luminal epithelium:	n/a	chr14:65769180-65769188
3	PAX5	chr14:65769389-65769905	GM12878	blood:	n/a	n/a
4	POLR2A	chr14:65768504-65770583	GM12878	blood:	n/a	n/a
5	POLR2A	chr14:65768458-65771398	GM12891	blood:	n/a	n/a
6	POLR2A	chr14:65768469-65771325	GM18951	blood:	n/a	n/a
7	POLR2A	chr14:65767150-65771470	GM12892	blood:	n/a	n/a
8	NFIC	chr14:65768050-65770972	GM12878	blood:	n/a	n/a
9	POLR2A	chr14:65767239-65771468	GM12892	blood:	n/a	n/a
10	POLR2A	chr14:65769268-65769632	H1-neurons	neurons:	n/a	n/a
11	POU2F2	chr14:65768420-65770035	GM12891	blood:	n/a	chr14:65769074-65769088 chr14:65769077-65769086
12	EBF1	chr14:65769175-65769982	GM12878	blood:	n/a	n/a
13	POLR2A	chr14:65767525-65772793	GM12878	blood:	n/a	n/a
14	POLR2A	chr14:65768350-65771408	GM12878	blood:	n/a	n/a
15	NFIC	chr14:65769183-65769789	ECC-1	luminal epithelium:	n/a	n/a
16	POLR2A	chr14:65767993-65772386	GM18505	blood:	n/a	n/a
17	RELA	chr14:65768445-65771188	GM12878	blood:	n/a	n/a
18	POLR2A	chr14:65767590-65772501	GM12892	blood:	n/a	n/a
19	STAT3	chr14:65769358-65769698	MCF10A-Er-Src	breast:	n/a	n/a
20	YY1	chr14:65769032-65769848	GM12892	blood:	n/a	n/a
21	POLR2A	chr14:65768552-65772630	Raji	blood:	n/a	n/a
22	CREB1	chr14:65768533-65770032	GM12878	blood:	n/a	n/a
23	WRNIP1	chr14:65768587-65770480	GM12878	blood:	n/a	n/a
24	BCLAF1	chr14:65768393-65770585	GM12878	blood:	n/a	n/a
25	SMC3	chr14:65768573-65770793	GM12878	blood:	n/a	n/a
26	POLR2A	chr14:65767806-65771462	GM12892	blood:	n/a	n/a
27	STAT3	chr14:65769348-65769687	MCF10A-Er-Src	breast:	n/a	n/a
28	POLR2A	chr14:65768763-65769492	HepG2	liver:	n/a	n/a
29	NFATC1	chr14:65768356-65771125	GM12878	blood:	n/a	n/a
30	FOXM1	chr14:65768441-65770694	GM12878	blood:	n/a	n/a
31	POLR2A	chr14:65768364-65771439	GM12891	blood:	n/a	n/a
32	BHLHE40	chr14:65768549-65769962	GM12878	blood:	n/a	n/a
33	STAT3	chr14:65769385-65769695	MCF10A-Er-Src	breast:	n/a	n/a
34	STAT5A	chr14:65768891-65770642	GM12878	blood:	n/a	chr14:65769178-65769186
35	PAX5	chr14:65769031-65770071	GM12878	blood:	n/a	n/a
36	CEBPB	chr14:65768286-65770719	GM12878	blood:	n/a	n/a
37	FOS	chr14:65769407-65769585	MCF10A-Er-Src	breast:	n/a	n/a
38	NFYB	chr14:65768595-65769557	GM12878	blood:	n/a	n/a
39	RUNX3	chr14:65768306-65771264	GM12878	blood:	n/a	n/a
40	RELA	chr14:65768464-65771262	GM18505	blood:	n/a	n/a
41	STAT5A	chr14:65768360-65771354	GM12878	blood:	n/a	chr14:65769178-65769186 chr14:65771114-65771126
42	MYC	chr14:65769369-65769525	MCF10A-Er-Src	breast:	n/a	n/a
43	ATF2	chr14:65768211-65770878	GM12878	blood:	n/a	n/a
44	POLR2A	chr14:65768433-65770569	GM12891	blood:	n/a	n/a
45	TCF12	chr14:65769129-65769799	ECC-1	luminal epithelium:	n/a	chr14:65769180-65769188
46	TAF1	chr14:65769314-65770020	GM12878	blood:	n/a	n/a
47	MTA3	chr14:65768424-65771359	GM12878	blood:	n/a	n/a
48	MAX	chr14:65769150-65769650	ECC-1	luminal epithelium:	n/a	n/a
49	BCLAF1	chr14:65768275-65771420	GM12878	blood:	n/a	chr14:65770652-65770665 chr14:65770644-65770657
50	TBP	chr14:65768353-65770905	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:65769045..65770910-chr14:65878599..65880667,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258760	TF binding region
ENSG00000033170	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1038239	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11846705	0.89[EUR][1000 genomes]
rs1256537	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1256541	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1256544	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17180994	0.86[EUR][1000 genomes]
rs2411915	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3986780	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4899175	0.89[EUR][1000 genomes]
rs7144530	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs8015222	0.86[EUR][1000 genomes]
rs8021946	0.86[EUR][1000 genomes]
rs8023016	0.86[EUR][1000 genomes]
rs899960	1.00[CEU][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832817	chr14:65637069-65810406	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
2	nsv832818	chr14:65706859-65882320	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
4	nsv515522	chr14:65746566-65771110	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65758800-65770000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr14:65758800-65773400	Weak transcription	Spleen	Spleen
3	chr14:65760000-65781000	Weak transcription	Primary B cells from cord blood	blood
4	chr14:65763200-65774200	Enhancers	Primary B cells from peripheral blood	blood
5	chr14:65763800-65771200	Enhancers	Fetal Intestine Small	intestine
6	chr14:65765000-65769800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr14:65766000-65771200	Enhancers	Fetal Intestine Large	intestine
8	chr14:65766000-65772400	Enhancers	Stomach Mucosa	stomach
9	chr14:65766400-65770600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr14:65766600-65771200	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr14:65767000-65769600	Weak transcription	Colonic Mucosa	Colon
12	chr14:65767200-65770200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr14:65767600-65769600	Flanking Active TSS	GM12878-XiMat	blood
14	chr14:65767600-65772800	Enhancers	Duodenum Mucosa	Duodenum
15	chr14:65768400-65772400	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr14:65768400-65772800	Enhancers	Primary T cells from cord blood	blood
17	chr14:65768600-65769600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr14:65768600-65769800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr14:65768600-65769800	Enhancers	K562	blood
20	chr14:65768600-65770000	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr14:65768600-65770200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr14:65768600-65770400	Enhancers	Thymus	Thymus
23	chr14:65768600-65770600	Enhancers	Small Intestine	intestine
24	chr14:65768600-65771200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr14:65768600-65771200	Enhancers	Pancreas	Pancrea
26	chr14:65768600-65771400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr14:65768600-65772000	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr14:65768600-65772400	Enhancers	Fetal Thymus	thymus
29	chr14:65768600-65772800	Enhancers	Primary T cells fromperipheralblood	blood
30	chr14:65768600-65773600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr14:65768800-65769800	Flanking Active TSS	HepG2	liver
32	chr14:65768800-65770400	Enhancers	NHDF-Ad	bronchial
33	chr14:65768800-65770600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr14:65768800-65771000	Enhancers	Fetal Stomach	stomach
35	chr14:65768800-65771200	Enhancers	Brain Hippocampus Middle	brain
36	chr14:65768800-65771200	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr14:65768800-65771200	Enhancers	Hela-S3	cervix
38	chr14:65768800-65772000	Enhancers	Brain Substantia Nigra	brain
39	chr14:65768800-65772200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr14:65769000-65770000	Enhancers	Brain Anterior Caudate	brain
41	chr14:65769000-65770600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr14:65769000-65770600	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr14:65769000-65770600	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr14:65769000-65770800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr14:65769000-65771000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr14:65769000-65771200	Enhancers	Brain Angular Gyrus	brain
47	chr14:65769000-65772400	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr14:65769200-65770000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr14:65769200-65770000	Enhancers	HSMM	muscle
50	chr14:65769200-65771000	Enhancers	HUES48 Cell Line	embryonic stem cell

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