Variant report

Variant	rs298990
Chromosome Location	chr4:119646673-119646674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10518322	0.83[CEU][hapmap];0.86[AMR][1000 genomes]
rs10518323	0.86[CEU][hapmap];0.86[AMR][1000 genomes]
rs10518324	0.86[CEU][hapmap];0.86[AMR][1000 genomes]
rs11098449	0.82[AMR][1000 genomes]
rs11098450	0.83[CEU][hapmap];0.86[AMR][1000 genomes]
rs11722833	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11730993	0.87[AMR][1000 genomes]
rs12500272	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12505513	0.82[CEU][hapmap];0.86[AMR][1000 genomes]
rs12509236	0.91[CEU][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12509654	0.95[CEU][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13109947	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13109966	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13114964	0.83[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13120798	0.83[CEU][hapmap];0.86[AMR][1000 genomes]
rs13130107	0.97[EUR][1000 genomes]
rs17050423	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs298976	0.99[EUR][1000 genomes]
rs298977	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs298980	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs298981	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs298989	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs298993	0.98[EUR][1000 genomes]
rs298997	0.99[EUR][1000 genomes]
rs299002	0.96[EUR][1000 genomes]
rs299003	0.96[EUR][1000 genomes]
rs299004	0.96[EUR][1000 genomes]
rs34371874	0.97[EUR][1000 genomes]
rs34384498	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34616305	0.86[AMR][1000 genomes]
rs34730066	0.86[AMR][1000 genomes]
rs35868882	0.84[AMR][1000 genomes]
rs3775836	0.87[AMR][1000 genomes]
rs399086	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs401950	0.95[EUR][1000 genomes]
rs428409	1.00[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs437027	0.99[EUR][1000 genomes]
rs439159	0.96[EUR][1000 genomes]
rs4834698	0.99[EUR][1000 genomes]
rs4834699	0.91[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7676832	0.86[AMR][1000 genomes]
rs960738	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs960739	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119607200-119659200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:119607800-119693800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr4:119608600-119674000	Weak transcription	Stomach Mucosa	stomach
4	chr4:119609200-119648600	Weak transcription	Fetal Heart	heart
5	chr4:119620000-119660200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr4:119625800-119718000	Weak transcription	Hela-S3	cervix
7	chr4:119626600-119648000	Weak transcription	Psoas Muscle	Psoas
8	chr4:119627400-119648600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr4:119627800-119648600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr4:119628000-119647000	Weak transcription	Brain Substantia Nigra	brain
11	chr4:119628000-119659800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr4:119628200-119647800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr4:119628400-119657600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:119630400-119674200	Weak transcription	A549	lung
15	chr4:119631600-119648800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:119631600-119650800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr4:119631800-119649800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr4:119632400-119646800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:119632400-119647000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr4:119632800-119647000	Weak transcription	Fetal Kidney	kidney
21	chr4:119632800-119648000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr4:119633200-119646800	Weak transcription	Primary B cells from peripheral blood	blood
23	chr4:119633200-119662800	Weak transcription	Brain Anterior Caudate	brain
24	chr4:119633400-119646800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:119633400-119667600	Weak transcription	Brain Germinal Matrix	brain
26	chr4:119634400-119660000	Weak transcription	Brain Angular Gyrus	brain
27	chr4:119634600-119648600	Weak transcription	Brain Hippocampus Middle	brain
28	chr4:119637800-119647000	Weak transcription	Fetal Brain Female	brain
29	chr4:119638400-119650200	Strong transcription	Osteobl	bone
30	chr4:119638400-119650600	Strong transcription	NH-A	brain
31	chr4:119638400-119650800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:119638600-119648800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr4:119638600-119650600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr4:119639400-119648600	Strong transcription	HSMM	muscle
35	chr4:119639600-119651600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr4:119640600-119662200	Strong transcription	Fetal Muscle Trunk	muscle
37	chr4:119640800-119692600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr4:119641200-119652600	Strong transcription	HSMMtube	muscle
39	chr4:119641200-119659600	Strong transcription	Fetal Intestine Large	intestine
40	chr4:119641400-119649200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr4:119641400-119649800	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr4:119641400-119650600	Strong transcription	NHDF-Ad	bronchial
43	chr4:119641600-119649000	Weak transcription	Fetal Brain Male	brain
44	chr4:119641600-119650800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:119641600-119659400	Strong transcription	Liver	Liver
46	chr4:119641600-119679800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr4:119641800-119650600	Strong transcription	HepG2	liver
48	chr4:119642000-119649800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr4:119642000-119650600	Strong transcription	HUVEC	blood vessel
50	chr4:119642000-119653200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links