Variant report

Variant	rs1263801
Chromosome Location	chr14:21978884-21978885
allele	C/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	POLR2A	chr14:21978749-21979958	K562	blood:	n/a	n/a
2	POLR2A	chr14:21978395-21979811	IMR90	lung:	n/a	n/a
3	E2F6	chr14:21978785-21979831	A549	lung:	n/a	chr14:21978909-21978916 chr14:21979443-21979458
4	MBD4	chr14:21978740-21979848	HepG2	liver:	n/a	n/a
5	POLR2A	chr14:21978731-21979913	K562	blood:	n/a	n/a
6	POLR2A	chr14:21978848-21980445	HepG2	liver:	n/a	n/a
7	MYC	chr14:21978858-21979890	K562	blood:	n/a	n/a
8	POLR2A	chr14:21978719-21979831	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr14:21978849-21979952	HL-60	blood:	n/a	n/a
10	REST	chr14:21978831-21979853	A549	lung:	n/a	chr14:21979486-21979496
11	POLR2A	chr14:21978261-21980520	MCF10A-Er-Src	breast:	n/a	n/a
12	MAX	chr14:21978877-21979789	A549	lung:	n/a	n/a
13	HEY1	chr14:21978752-21979971	HepG2	liver:	n/a	n/a
14	MXI1	chr14:21978674-21979766	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr14:21978793-21979938	PBDE	blood:	n/a	n/a
16	POLR2A	chr14:21978675-21979996	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr14:21978879-21979796	HepG2	liver:	n/a	n/a
18	EGR1	chr14:21978787-21979862	MCF-7	breast:	n/a	n/a
19	MAX	chr14:21978866-21979813	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr14:21978867-21979831	GM12878	blood:	n/a	n/a
21	POLR2A	chr14:21978809-21979802	GM12878	blood:	n/a	n/a
22	POLR2A	chr14:21978865-21979765	A549	lung:	n/a	n/a
23	TAF1	chr14:21978774-21979945	A549	lung:	n/a	n/a
24	POLR2A	chr14:21978541-21979947	HUVEC	blood vessel:	n/a	n/a
25	YY1	chr14:21978820-21980254	HepG2	liver:	n/a	chr14:21979651-21979670 chr14:21979678-21979697 chr14:21979683-21979691 chr14:21979629-21979651 chr14:21979653-21979675 chr14:21979680-21979690 chr14:21979656-21979664 chr14:21979680-21979702 chr14:21979653-21979663 chr14:21979632-21979640
26	POLR2A	chr14:21978834-21979762	GM12878	blood:	n/a	n/a
27	TAF1	chr14:21978879-21979820	ECC-1	luminal epithelium:	n/a	n/a
28	TAF1	chr14:21978699-21979801	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr14:21978516-21979952	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr14:21978849-21980164	Hela-S3	cervix:	n/a	n/a
31	GABPA	chr14:21978838-21979840	MCF-7	breast:	n/a	chr14:21979673-21979682
32	POLR2A	chr14:21978863-21979873	PFSK-1	brain:	n/a	n/a
33	POLR2A	chr14:21978879-21979912	NB4	blood:	n/a	n/a
34	POLR2A	chr14:21978638-21980001	GM12892	blood:	n/a	n/a
35	MAZ	chr14:21978800-21979774	K562	blood:	n/a	n/a
36	CHD1	chr14:21978773-21978974	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr14:21978866-21979912	GM19193	blood:	n/a	n/a
38	HDAC2	chr14:21978756-21979719	HepG2	liver:	n/a	chr14:21979673-21979682
39	POLR2A	chr14:21978629-21979906	GM12891	blood:	n/a	n/a
40	POLR2A	chr14:21978482-21979989	GM12892	blood:	n/a	n/a
41	BRCA1	chr14:21978705-21979810	Hela-S3	cervix:	n/a	n/a
42	MXI1	chr14:21978669-21979808	GM12878	blood:	n/a	n/a
43	CREB1	chr14:21978805-21979917	HepG2	liver:	n/a	n/a
44	MAX	chr14:21978821-21979821	SK-N-SH	brain:	n/a	n/a
45	YY1	chr14:21978814-21980000	K562	blood:	n/a	chr14:21979651-21979670 chr14:21979678-21979697 chr14:21979683-21979691 chr14:21979629-21979651 chr14:21979653-21979675 chr14:21979680-21979690 chr14:21979656-21979664 chr14:21979680-21979702 chr14:21979653-21979663 chr14:21979632-21979640
46	HCFC1	chr14:21978619-21980706	Hela-S3	cervix:	n/a	n/a
47	TAF1	chr14:21978861-21980025	ECC-1	luminal epithelium:	n/a	n/a
48	MAX	chr14:21978723-21979795	A549	lung:	n/a	n/a
49	CREB1	chr14:21978804-21979871	HepG2	liver:	n/a	n/a
50	GABPA	chr14:21978799-21979937	A549	lung:	n/a	chr14:21979673-21979682

No.	Distal block	Cell Line	Cell type
1	chr14:21976926..21983845-chr14:21991695..21998209,25	K562	blood:
2	chr14:21978010..21981856-chr14:21985023..21989241,7	MCF-7	breast:
3	chr14:21977989..21980901-chr14:22001631..22005636,4	K562	blood:
4	chr14:21851357..21853196-chr14:21978251..21980149,2	K562	blood:
5	chr14:21927480..21929708-chr14:21977698..21979335,2	K562	blood:
6	chr14:21943182..21946742-chr14:21976824..21981257,10	MCF-7	breast:
7	chr14:21969916..21972018-chr14:21978032..21980758,3	K562	blood:
8	chr14:21943174..21944974-chr14:21977836..21979361,2	K562	blood:
9	chr14:21924214..21926252-chr14:21977009..21978995,2	K562	blood:
10	chr14:21943699..21946735-chr14:21977733..21982256,4	MCF-7	breast:
11	chr14:21977163..21984004-chr14:21985497..21991656,11	K562	blood:
12	chr14:21972318..21975113-chr14:21978008..21980143,3	K562	blood:
13	chr14:21923462..21925701-chr14:21977921..21979566,3	MCF-7	breast:
14	chr14:21977943..21985344-chr14:21985568..21995608,22	MCF-7	breast:
15	chr14:21851427..21853981-chr14:21978345..21981165,2	MCF-7	breast:
16	chr14:21921735..21926252-chr14:21977495..21980798,4	K562	blood:
17	chr14:21943174..21947446-chr14:21976603..21980796,8	K562	blood:
18	chr14:21953304..21957637-chr14:21977622..21980273,4	K562	blood:
19	chr14:21977974..21981747-chr14:21991693..21997000,9	MCF-7	breast:
20	chr14:21958167..21960481-chr14:21978207..21981018,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SALL2-1	chr14:21978797-21979122	NONHSAT035696
2	lnc-SALL2-1	chr14:21978710-21979055	NONHSAT035695

Variant related genes	Relation type
METTL3	TF binding region
ENSG00000092203	Chromatin interaction
ENSG00000129472	Chromatin interaction
ENSG00000100888	Chromatin interaction
ENSG00000260830	Chromatin interaction
ENSG00000165821	Chromatin interaction
ENSG00000257096	Chromatin interaction
ENSG00000092201	Chromatin interaction
ENSG00000165819	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10135215	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs1060722	0.84[AMR][1000 genomes]
rs11156994	0.83[AMR][1000 genomes]
rs1139130	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12431578	0.82[AMR][1000 genomes]
rs12435421	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs1263791	0.96[CEU][hapmap];0.85[YRI][hapmap]
rs1263793	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1263796	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1263799	0.96[CEU][hapmap];0.83[JPT][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12889546	0.81[AMR][1000 genomes]
rs2242526	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs2297093	0.96[CEU][hapmap];0.83[AMR][1000 genomes]
rs28526734	0.83[AMR][1000 genomes]
rs28608673	0.83[AMR][1000 genomes]
rs28694613	0.84[AMR][1000 genomes]
rs3737049	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs4296176	0.81[AMR][1000 genomes]
rs7150948	0.81[AMR][1000 genomes]
rs7617	0.84[AMR][1000 genomes]
rs8004916	0.80[AMR][1000 genomes]
rs933192	0.96[CEU][hapmap];0.83[AMR][1000 genomes]
rs966602	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]

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	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
2	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
3	nsv1036762	chr14:21507093-22101805	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	nsv541976	chr14:21507093-22101805	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	esv3518898	chr14:21805983-22077584	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	esv3518899	chr14:21805983-22077584	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
7	nsv1054013	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv541991	chr14:21868964-21992109	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv530011	chr14:21876973-21985341	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv2422459	chr14:21931624-22169502	Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1263801	METTL3	Cis_1M	lymphoblastoid	RTeQTL
rs1263801	TOX4	cis	brain	BrainEAC
rs1263801	TOX4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21977600-21979000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
2	chr14:21977600-21979000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr14:21977800-21979000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
4	chr14:21977800-21980000	Active TSS	K562	blood
5	chr14:21977800-21980200	Active TSS	H1 Cell Line	embryonic stem cell
6	chr14:21977800-21980200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr14:21977800-21980200	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr14:21977800-21980400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr14:21978000-21979000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr14:21978000-21979000	Flanking Active TSS	Brain Germinal Matrix	brain
11	chr14:21978000-21979000	Flanking Active TSS	Colon Smooth Muscle	Colon
12	chr14:21978000-21979000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
13	chr14:21978000-21979000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr14:21978000-21979200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr14:21978000-21979400	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr14:21978000-21980200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr14:21978000-21980200	Active TSS	Psoas Muscle	Psoas
18	chr14:21978000-21980400	Active TSS	NHLF	lung
19	chr14:21978200-21979000	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
20	chr14:21978200-21979000	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr14:21978200-21979000	Flanking Active TSS	Liver	Liver
22	chr14:21978200-21979000	Flanking Active TSS	Brain Anterior Caudate	brain
23	chr14:21978200-21979000	Flanking Active TSS	Brain Hippocampus Middle	brain
24	chr14:21978200-21979000	Flanking Active TSS	Brain Substantia Nigra	brain
25	chr14:21978200-21979000	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr14:21978200-21979000	Flanking Active TSS	Stomach Smooth Muscle	stomach
27	chr14:21978200-21979400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr14:21978200-21979600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr14:21978200-21979600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr14:21978200-21979800	Active TSS	Fetal Thymus	thymus
31	chr14:21978200-21980000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr14:21978200-21980200	Active TSS	Right Atrium	heart
33	chr14:21978200-21980200	Active TSS	Right Ventricle	heart
34	chr14:21978200-21980200	Active TSS	HMEC	breast
35	chr14:21978200-21980200	Active TSS	HSMM	muscle
36	chr14:21978200-21980200	Active TSS	NH-A	brain
37	chr14:21978200-21980400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr14:21978200-21980400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr14:21978200-21980600	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr14:21978400-21979000	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr14:21978400-21979000	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr14:21978400-21979000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
43	chr14:21978400-21979000	Flanking Active TSS	Fetal Stomach	stomach
44	chr14:21978400-21979200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
45	chr14:21978400-21979200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr14:21978400-21979200	Flanking Active TSS	Brain Angular Gyrus	brain
47	chr14:21978400-21979600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr14:21978400-21979600	Active TSS	Fetal Muscle Trunk	muscle
49	chr14:21978400-21980000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr14:21978400-21980000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell

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