Variant report

Variant	rs2741732
Chromosome Location	chr14:21457945-21457946
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	POLR2A	chr14:21457930-21458442	A549	lung:	n/a	n/a
2	HDAC2	chr14:21457831-21458795	HepG2	liver:	n/a	n/a
3	POLR2A	chr14:21457929-21458341	H1-hESC	embryonic stem cell:	n/a	n/a
4	GABPA	chr14:21457694-21458726	Hela-S3	cervix:	n/a	chr14:21458597-21458604
5	POLR2A	chr14:21457931-21458402	GM12891	blood:	n/a	n/a
6	SIX5	chr14:21457695-21458512	A549	lung:	n/a	n/a
7	POLR2A	chr14:21457513-21458807	GM12892	blood:	n/a	n/a
8	BCL3	chr14:21457761-21458396	A549	lung:	n/a	n/a
9	SP1	chr14:21457713-21458338	H1-hESC	embryonic stem cell:	n/a	chr14:21458013-21458034
10	TAF1	chr14:21457941-21458621	GM12878	blood:	n/a	n/a
11	RFX5	chr14:21457662-21458305	GM12878	blood:	n/a	n/a
12	POLR2A	chr14:21457600-21458728	GM12891	blood:	n/a	n/a
13	ZNF143	chr14:21457804-21458762	Hela-S3	cervix:	n/a	chr14:21458315-21458325
14	POLR2A	chr14:21457906-21458630	GM12878	blood:	n/a	n/a
15	NFIC	chr14:21457911-21458711	HepG2	liver:	n/a	chr14:21458025-21458041 chr14:21458015-21458043
16	POU2F2	chr14:21457915-21458426	GM12891	blood:	n/a	n/a
17	FOS	chr14:21457932-21458214	MCF10A-Er-Src	breast:	n/a	n/a
18	MXI1	chr14:21457370-21458948	IMR90	lung:	n/a	n/a
19	POLR2A	chr14:21457305-21458707	GM18505	blood:	n/a	n/a
20	ZEB1	chr14:21457921-21458219	GM12878	blood:	n/a	chr14:21457987-21457995
21	ZKSCAN1	chr14:21457761-21458647	Hela-S3	cervix:	n/a	n/a
22	SIX5	chr14:21457885-21458368	A549	lung:	n/a	n/a
23	POLR2A	chr14:21457589-21458730	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr14:21457255-21458677	PBDE	blood:	n/a	n/a
25	EGR1	chr14:21457715-21458101	K562	blood:	n/a	n/a
26	ELF1	chr14:21457637-21458453	SK-N-SH	brain:	n/a	n/a
27	E2F4	chr14:21457663-21458767	MCF10A-Er-Src	breast:	n/a	chr14:21458549-21458561 chr14:21458315-21458325 chr14:21458553-21458560 chr14:21458553-21458560 chr14:21458553-21458560
28	POLR2A	chr14:21456785-21458854	K562	blood:	n/a	n/a
29	MYBL2	chr14:21457911-21458855	HepG2	liver:	n/a	n/a
30	SIN3AK20	chr14:21457666-21458931	MCF-7	breast:	n/a	n/a
31	SIX5	chr14:21457926-21458279	K562	blood:	n/a	n/a
32	FOS	chr14:21457860-21458235	GM12878	blood:	n/a	n/a
33	TCF7L2	chr14:21457939-21458692	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr14:21457618-21458665	GM12892	blood:	n/a	n/a
35	SP1	chr14:21457709-21458719	A549	lung:	n/a	chr14:21458013-21458034
36	SIX5	chr14:21457918-21458301	H1-hESC	embryonic stem cell:	n/a	n/a
37	TAF1	chr14:21457917-21458824	A549	lung:	n/a	n/a
38	POLR2A	chr14:21457659-21458688	GM19193	blood:	n/a	n/a
39	GABPA	chr14:21457874-21458466	GM12878	blood:	n/a	n/a
40	POLR2A	chr14:21457575-21458710	Hela-S3	cervix:	n/a	n/a
41	HCFC1	chr14:21457160-21458907	Hela-S3	cervix:	n/a	n/a
42	RUNX3	chr14:21457893-21458362	GM12878	blood:	n/a	n/a
43	POLR2A	chr14:21457942-21458427	PANC-1	pancreas:	n/a	n/a
44	POLR2A	chr14:21457629-21458589	K562	blood:	n/a	n/a
45	POLR2A	chr14:21457929-21458673	PFSK-1	brain:	n/a	n/a
46	NFYB	chr14:21457740-21458288	Hela-S3	cervix:	n/a	chr14:21458020-21458035 chr14:21458021-21458035 chr14:21458023-21458033 chr14:21458020-21458035 chr14:21458053-21458063
47	HDAC2	chr14:21457733-21458872	MCF-7	breast:	n/a	chr14:21457743-21457757 chr14:21457740-21457754
48	POLR2A	chr14:21457611-21458797	K562	blood:	n/a	n/a
49	POLR2A	chr14:21457629-21458722	K562	blood:	n/a	n/a
50	CREB1	chr14:21457903-21458206	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:21452044..21453634-chr14:21457203..21461213,3	MCF-7	breast:
2	chr14:21450582..21454134-chr14:21456083..21458920,5	K562	blood:
3	chr14:21456741..21458593-chr14:21486846..21489744,2	MCF-7	breast:
4	chr14:21452633..21454134-chr14:21456113..21458171,2	K562	blood:
5	chr14:21457358..21458225-chr4:52708716..52709599,2	NB4	blood:
6	chr14:21456868..21460721-chr14:21463900..21468435,6	MCF-7	breast:
7	chr14:20921981..20924966-chr14:21455832..21458950,3	MCF-7	breast:
8	chr14:21457621..21458602-chr19:33793197..33793833,2	Hela-S3	cervix:
9	chr14:21457560..21458554-chr21:28215410..28216217,2	Hela-S3	cervix:

Variant related genes	Relation type
METTL17	TF binding region
ENSG00000258599	TF binding region
ENSG00000165795	Chromatin interaction
ENSG00000258471	Chromatin interaction
ENSG00000092094	Chromatin interaction
ENSG00000100823	Chromatin interaction
ENSG00000267296	Chromatin interaction
ENSG00000245848	Chromatin interaction
ENSG00000165794	Chromatin interaction
ENSG00000154734	Chromatin interaction
ENSG00000230259	Chromatin interaction
ENSG00000109184	Chromatin interaction
ENSG00000258599	Chromatin interaction
ENSG00000165792	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2741727	0.88[ASN][1000 genomes]
rs2741729	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2741737	1.00[CEU][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2771334	0.87[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2771335	0.87[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs2771340	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2771342	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2771346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2783786	0.87[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.83[ASN][1000 genomes]
rs3790067	1.00[LWK][hapmap]

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	esv2758349	chr14:21216108-21471614	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759972	chr14:21216108-21471614	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv427936	chr14:21216108-21531783	Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv428293	chr14:21216108-21531783	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
5	nsv832740	chr14:21332060-21545052	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
6	nsv470622	chr14:21338824-21469151	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
7	nsv563847	chr14:21338824-21469151	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
8	nsv530009	chr14:21377022-22044608	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
9	nsv530769	chr14:21407536-22139126	Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
10	nsv901475	chr14:21426282-21465489	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2741732	OSGEP	cis	cerebellum	SCAN
rs2741732	METTL17	cis	Whole Blood	GTEx
rs2741732	RBM23	cis	cerebellum	SCAN
rs2741732	OR4K5	cis	parietal	SCAN
rs2741732	SUPT16H	cis	parietal	SCAN
rs2741732	METTL17	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21457200-21458000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr14:21457200-21458000	Enhancers	Placenta	Placenta
3	chr14:21457200-21458600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr14:21457200-21458800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr14:21457200-21458800	Active TSS	Colonic Mucosa	Colon
6	chr14:21457200-21458800	Active TSS	Fetal Brain Male	brain
7	chr14:21457400-21458000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr14:21457400-21458400	Active TSS	Cortex derived primary cultured neurospheres	brain
9	chr14:21457400-21458600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr14:21457400-21458600	Active TSS	Fetal Brain Female	brain
11	chr14:21457400-21459200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr14:21457400-21459200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr14:21457400-21459400	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr14:21457400-21459400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr14:21457400-21459600	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr14:21457600-21458000	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr14:21457600-21458000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr14:21457600-21458000	Active TSS	Right Atrium	heart
19	chr14:21457600-21458200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr14:21457600-21458200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr14:21457600-21458200	Weak transcription	Fetal Heart	heart
22	chr14:21457600-21458200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr14:21457600-21458200	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr14:21457600-21458200	Weak transcription	Small Intestine	intestine
25	chr14:21457600-21458200	Weak transcription	Stomach Mucosa	stomach
26	chr14:21457600-21458200	Active TSS	HepG2	liver
27	chr14:21457600-21458400	Active TSS	Primary B cells from cord blood	blood
28	chr14:21457600-21458400	Active TSS	Primary B cells from peripheral blood	blood
29	chr14:21457600-21458400	Active TSS	Primary T cells fromperipheralblood	blood
30	chr14:21457600-21458400	Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr14:21457600-21458400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr14:21457600-21458400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr14:21457600-21458400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
34	chr14:21457600-21458400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
35	chr14:21457600-21458400	Active TSS	Adipose Nuclei	Adipose
36	chr14:21457600-21458400	Active TSS	Brain Angular Gyrus	brain
37	chr14:21457600-21458400	Active TSS	Brain Cingulate Gyrus	brain
38	chr14:21457600-21458400	Active TSS	Duodenum Mucosa	Duodenum
39	chr14:21457600-21458400	Active TSS	Rectal Mucosa Donor 31	rectum
40	chr14:21457600-21458400	Active TSS	Thymus	Thymus
41	chr14:21457600-21458400	Active TSS	Monocytes-CD14+_RO01746	blood
42	chr14:21457600-21458600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr14:21457600-21458600	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr14:21457600-21458600	Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr14:21457600-21458600	Active TSS	Primary T killer memory cells from peripheral blood	blood
46	chr14:21457600-21458600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr14:21457600-21458600	Active TSS	Brain Anterior Caudate	brain
48	chr14:21457600-21458600	Active TSS	Brain Hippocampus Middle	brain
49	chr14:21457600-21458600	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr14:21457600-21458600	Active TSS	Brain Substantia Nigra	brain

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