Variant report

Variant	rs298980
Chromosome Location	chr4:119607376-119607377
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119199307..119202288-chr4:119603050..119607934,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269893	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10014208	0.84[GIH][hapmap]
rs10518322	0.86[CEU][hapmap]
rs10518323	0.86[CEU][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap]
rs10518324	0.86[CEU][hapmap];0.81[GIH][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap]
rs11098450	0.86[CEU][hapmap]
rs11722833	0.95[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs11736024	0.84[GIH][hapmap];0.82[MKK][hapmap]
rs12500272	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12505513	0.82[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap]
rs12509236	0.91[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs12509654	0.95[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.96[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs13109947	0.81[EUR][1000 genomes]
rs13109966	0.81[EUR][1000 genomes]
rs13114964	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs13120798	0.86[CEU][hapmap]
rs13130107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17050423	0.81[EUR][1000 genomes]
rs298976	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298977	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs298981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs298989	1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs298990	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs298993	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs298997	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299002	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299003	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs299004	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34371874	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34384498	0.81[EUR][1000 genomes]
rs3775836	0.84[GIH][hapmap]
rs399086	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs401950	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs428409	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs437027	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs439159	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4834698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4834699	0.91[CEU][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs960738	0.98[GIH][hapmap];0.86[JPT][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap]
rs960739	0.95[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv427693	chr4:119493919-119674742	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs298980	METTL14	cis	lymphoblastoid	seeQTL
rs298980	METTL14	cis	cerebellum	SCAN
rs298980	KIAA1627	cis	multi-tissue	Pritchard
rs298980	USP53	cis	cerebellum	SCAN
rs298980	METTL14	cis	brain	seeQTL
rs298980	METTL14	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119605200-119607400	Active TSS	Hela-S3	cervix
2	chr4:119605800-119607400	Active TSS	HMEC	breast
3	chr4:119605800-119607800	Active TSS	A549	lung
4	chr4:119606000-119607400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr4:119606000-119607400	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr4:119606000-119607400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr4:119606000-119607400	Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr4:119606000-119607400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:119606000-119607400	Active TSS	Brain Angular Gyrus	brain
10	chr4:119606000-119607400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:119606000-119607400	Active TSS	Fetal Brain Male	brain
12	chr4:119606000-119607400	Active TSS	Fetal Heart	heart
13	chr4:119606000-119607400	Active TSS	Fetal Kidney	kidney
14	chr4:119606000-119607400	Active TSS	Placenta	Placenta
15	chr4:119606000-119607400	Active TSS	Fetal Stomach	stomach
16	chr4:119606000-119607400	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr4:119606000-119607400	Active TSS	GM12878-XiMat	blood
18	chr4:119606000-119607400	Active TSS	HSMMtube	muscle
19	chr4:119606000-119607400	Active TSS	NHDF-Ad	bronchial
20	chr4:119606000-119607600	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr4:119606000-119607600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:119606000-119607600	Active TSS	Muscle Satellite Cultured Cells	--
23	chr4:119606000-119607600	Active TSS	Colonic Mucosa	Colon
24	chr4:119606000-119607600	Active TSS	Fetal Brain Female	brain
25	chr4:119606000-119607600	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr4:119606000-119607600	Active TSS	Fetal Muscle Trunk	muscle
27	chr4:119606000-119607600	Active TSS	Left Ventricle	heart
28	chr4:119606000-119607600	Active TSS	Right Ventricle	heart
29	chr4:119606000-119607600	Active TSS	Stomach Smooth Muscle	stomach
30	chr4:119606000-119607600	Active TSS	K562	blood
31	chr4:119606000-119607600	Active TSS	NHEK	skin
32	chr4:119606000-119607800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr4:119606000-119607800	Active TSS	Psoas Muscle	Psoas
34	chr4:119606000-119607800	Active TSS	Right Atrium	heart
35	chr4:119606000-119608000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:119606000-119608200	Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr4:119606000-119608400	Active TSS	Brain Germinal Matrix	brain
38	chr4:119606200-119607400	Active TSS	H9 Cell Line	embryonic stem cell
39	chr4:119606200-119607400	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr4:119606200-119607400	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr4:119606200-119607400	Active TSS	Breast Myoepithelial Primary Cells	Breast
42	chr4:119606200-119607400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr4:119606200-119607400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:119606200-119607400	Active TSS	Fetal Intestine Small	intestine
45	chr4:119606200-119607400	Active TSS	Placenta Amnion	Placenta Amnion
46	chr4:119606200-119607400	Active TSS	Stomach Mucosa	stomach
47	chr4:119606200-119607400	Active TSS	HSMM	muscle
48	chr4:119606200-119607600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr4:119606200-119607600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr4:119606200-119607600	Active TSS	HUES48 Cell Line	embryonic stem cell

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