Variant report

Variant	rs298977
Chromosome Location	chr4:119619836-119619837
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119612053..119615393-chr4:119619067..119621438,3	K562	blood:
2	chr4:119609732..119613553-chr4:119618798..119622906,4	K562	blood:
3	chr4:119605423..119607915-chr4:119618524..119621150,3	K562	blood:
4	chr4:119618502..119620267-chr4:119631410..119633788,2	K562	blood:

Variant related genes	Relation type
ENSG00000145388	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

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];0.98[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	0.91[EUR][1000 genomes]
rs12505513	0.82[CEU][hapmap];0.84[GIH][hapmap];0.91[TSI][hapmap]
rs12509236	1.00[ASW][hapmap];0.91[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12509654	0.95[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];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[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17050423	0.81[EUR][1000 genomes]
rs298976	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298980	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];0.95[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];0.99[ASN][1000 genomes]
rs298989	0.97[EUR][1000 genomes]
rs298990	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs298993	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs298997	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs299002	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299003	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs299004	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34371874	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34384498	0.81[EUR][1000 genomes]
rs3775836	0.84[GIH][hapmap]
rs399086	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs401950	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs428409	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs437027	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs439159	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4834698	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs298977	METTL14	cis	lymphoblastoid	seeQTL
rs298977	USP53	cis	cerebellum	SCAN
rs298977	KIAA1627	cis	multi-tissue	Pritchard
rs298977	WLS	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119607000-119644800	Weak transcription	Small Intestine	intestine
2	chr4:119607200-119659200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:119607800-119625600	Weak transcription	Aorta	Aorta
4	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr4:119608000-119645000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr4:119608600-119635200	Strong transcription	Fetal Thymus	thymus
7	chr4:119608600-119635800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:119608600-119674000	Weak transcription	Stomach Mucosa	stomach
9	chr4:119608800-119625400	Weak transcription	HSMMtube	muscle
10	chr4:119608800-119635000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr4:119609000-119620000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr4:119609000-119620400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr4:119609000-119620800	Strong transcription	Liver	Liver
14	chr4:119609000-119621200	Strong transcription	Osteobl	bone
15	chr4:119609000-119622600	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr4:119609000-119628200	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr4:119609000-119633200	Strong transcription	Placenta	Placenta
18	chr4:119609000-119633400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:119609000-119633400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:119609000-119633800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr4:119609000-119634400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr4:119609000-119634800	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr4:119609000-119635000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr4:119609000-119635000	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr4:119609000-119636000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr4:119609000-119636200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr4:119609200-119620600	Strong transcription	Duodenum Mucosa	Duodenum
28	chr4:119609200-119623400	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr4:119609200-119633400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:119609200-119634400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr4:119609200-119634800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr4:119609200-119635600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:119609200-119635600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr4:119609200-119635800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr4:119609200-119636200	Strong transcription	Adipose Nuclei	Adipose
36	chr4:119609200-119648600	Weak transcription	Fetal Heart	heart
37	chr4:119609400-119622800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:119609400-119633400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr4:119609400-119635600	Strong transcription	Dnd41	blood
40	chr4:119610000-119621000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr4:119610200-119628000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:119610400-119620200	Strong transcription	Fetal Lung	lung
43	chr4:119610400-119620400	Strong transcription	NH-A	brain
44	chr4:119610400-119628400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr4:119610400-119628600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr4:119611600-119625400	Weak transcription	Ovary	ovary
47	chr4:119611600-119625600	Weak transcription	Fetal Brain Male	brain
48	chr4:119611800-119625600	Weak transcription	Lung	lung
49	chr4:119611800-119625600	Weak transcription	Pancreas	Pancrea
50	chr4:119612000-119620000	Strong transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links