Variant report

Variant	rs298992
Chromosome Location	chr4:119641941-119641942
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:119636289..119638800-chr4:119641719..119643519,2	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1064034	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11735991	0.95[CEU][hapmap];0.80[EUR][1000 genomes]
rs13127508	0.95[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs167246	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2200517	0.90[CEU][hapmap]
rs2288306	0.95[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs2631147	0.90[CEU][hapmap]
rs298974	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs298975	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs298983	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs298984	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs298987	0.99[EUR][1000 genomes]
rs298991	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs298994	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs298995	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298996	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs298998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs299005	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs366656	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs368669	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs419292	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4340779	0.95[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs606665	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6822035	0.85[GIH][hapmap];0.86[TSI][hapmap]
rs6828577	0.95[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs6854328	0.95[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs7697022	0.95[CEU][hapmap];0.85[JPT][hapmap];0.93[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs298992	METTL14	cis	parietal	SCAN
rs298992	METTL14	cis	cerebellum	SCAN

Chromatin state (count:124 , 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	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr4:119608000-119645000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr4:119608600-119674000	Weak transcription	Stomach Mucosa	stomach
6	chr4:119609200-119648600	Weak transcription	Fetal Heart	heart
7	chr4:119620000-119660200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
9	chr4:119626600-119646000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:119626600-119648000	Weak transcription	Psoas Muscle	Psoas
11	chr4:119626800-119642200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:119626800-119644800	Weak transcription	Aorta	Aorta
13	chr4:119627200-119645000	Weak transcription	Spleen	Spleen
14	chr4:119627400-119645200	Weak transcription	Gastric	stomach
15	chr4:119627400-119645600	Weak transcription	Pancreas	Pancrea
16	chr4:119627400-119648600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:119627800-119642000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr4:119627800-119646200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr4:119627800-119648600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr4:119628000-119646400	Weak transcription	Colon Smooth Muscle	Colon
21	chr4:119628000-119647000	Weak transcription	Brain Substantia Nigra	brain
22	chr4:119628000-119659800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:119628200-119647800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:119628400-119657600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr4:119629400-119642200	Weak transcription	Lung	lung
26	chr4:119629400-119642600	Weak transcription	Fetal Intestine Small	intestine
27	chr4:119629400-119644400	Weak transcription	Ovary	ovary
28	chr4:119630400-119674200	Weak transcription	A549	lung
29	chr4:119631400-119644400	Weak transcription	Colonic Mucosa	Colon
30	chr4:119631600-119644400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr4:119631600-119645200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:119631600-119648800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr4:119631600-119650800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr4:119631800-119642000	Weak transcription	Left Ventricle	heart
35	chr4:119631800-119642200	Weak transcription	NHLF	lung
36	chr4:119631800-119645000	Weak transcription	Right Ventricle	heart
37	chr4:119631800-119645400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr4:119631800-119646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr4:119631800-119646000	Weak transcription	Thymus	Thymus
40	chr4:119631800-119649800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr4:119632000-119644800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr4:119632000-119646200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:119632400-119644800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr4:119632400-119646600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr4:119632400-119646800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr4:119632400-119647000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr4:119632600-119642000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr4:119632600-119642200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr4:119632600-119646000	Weak transcription	K562	blood
50	chr4:119632800-119642400	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links