Variant report

Variant	rs2297093
Chromosome Location	chr14:21955356-21955357
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	CEBPB	chr14:21954795-21955377	IMR90	lung:	n/a	chr14:21955213-21955224 chr14:21955212-21955223

No.	Distal block	Cell Line	Cell type
1	chr14:21948837..21951421-chr14:21953212..21956640,4	MCF-7	breast:
2	chr14:21941797..21947093-chr14:21954513..21961521,11	MCF-7	breast:
3	chr14:21954693..21956685-chr14:21971149..21973765,2	MCF-7	breast:
4	chr14:21953304..21957637-chr14:21977622..21980273,4	K562	blood:

Variant related genes	Relation type
TOX4	TF binding region
ENSG00000129472	Chromatin interaction
ENSG00000092203	Chromatin interaction
ENSG00000165819	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10135215	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060722	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061031	0.86[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs11156994	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1139130	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12431578	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12435421	1.00[ASW][hapmap];1.00[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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1263791	1.00[CEU][hapmap]
rs1263793	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1263796	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1263799	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1263801	0.96[CEU][hapmap];0.83[AMR][1000 genomes]
rs12880402	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12889546	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2282046	0.81[TSI][hapmap];0.93[YRI][hapmap]
rs28526734	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28608673	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28694613	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737049	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737050	0.86[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs4296176	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6571850	0.86[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs6571851	0.80[ASN][1000 genomes]
rs7150948	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7617	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8004916	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs933192	0.87[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs966602	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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
11	esv994931	chr14:21947144-21956367	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
12	esv3402606	chr14:21950812-21956610	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	esv3486915	chr14:21951462-21955760	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	esv3381254	chr14:21951637-21955985	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
15	esv3486916	chr14:21951837-21955660	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
16	esv2506236	chr14:21952194-21955404	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2297093	METTL3	Cis_1M	lymphoblastoid	RTeQTL
rs2297093	METTL3	cis	lymphoblastoid	seeQTL
rs2297093	TOX4	Cis_1M	lymphoblastoid	RTeQTL
rs2297093	LTB4R	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:21946000-21960600	Weak transcription	Small Intestine	intestine
2	chr14:21946200-21955600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:21946200-21955600	Weak transcription	Gastric	stomach
4	chr14:21946200-21955600	Weak transcription	Left Ventricle	heart
5	chr14:21946200-21955600	Weak transcription	Ovary	ovary
6	chr14:21946200-21955600	Weak transcription	Thymus	Thymus
7	chr14:21946200-21977600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr14:21946400-21955400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr14:21946400-21955600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr14:21946400-21958000	Weak transcription	Pancreas	Pancrea
11	chr14:21946400-21958800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr14:21946400-21960800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr14:21946400-21971400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr14:21946600-21955400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr14:21946600-21955400	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr14:21946600-21955600	Weak transcription	Brain Germinal Matrix	brain
17	chr14:21946600-21955600	Weak transcription	Colonic Mucosa	Colon
18	chr14:21946600-21955600	Weak transcription	Fetal Muscle Leg	muscle
19	chr14:21946600-21955600	Weak transcription	Psoas Muscle	Psoas
20	chr14:21946600-21955600	Weak transcription	Right Ventricle	heart
21	chr14:21946600-21955600	Weak transcription	Spleen	Spleen
22	chr14:21946600-21955800	Weak transcription	Fetal Brain Female	brain
23	chr14:21946600-21958000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr14:21946600-21960400	Weak transcription	Stomach Mucosa	stomach
25	chr14:21946600-21960800	Weak transcription	Aorta	Aorta
26	chr14:21946800-21955400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr14:21946800-21955600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr14:21946800-21955600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr14:21946800-21955600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr14:21946800-21955600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr14:21946800-21955600	Weak transcription	A549	lung
32	chr14:21946800-21955600	Weak transcription	GM12878-XiMat	blood
33	chr14:21946800-21955600	Weak transcription	NHEK	skin
34	chr14:21946800-21956200	Weak transcription	NH-A	brain
35	chr14:21946800-21956400	Weak transcription	Hela-S3	cervix
36	chr14:21946800-21956800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr14:21946800-21956800	Weak transcription	Brain Angular Gyrus	brain
38	chr14:21946800-21956800	Weak transcription	HMEC	breast
39	chr14:21946800-21959000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr14:21946800-21959000	Weak transcription	Fetal Brain Male	brain
41	chr14:21946800-21960800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr14:21947000-21955400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr14:21947000-21955400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr14:21947000-21955600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr14:21947000-21955600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr14:21947000-21955600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr14:21947000-21955600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr14:21947000-21955600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr14:21947000-21955600	Weak transcription	Brain Substantia Nigra	brain
50	chr14:21947000-21955600	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links