Variant report

Variant	rs1980718
Chromosome Location	chr3:119641266-119641267
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119640713..119642665-chr3:119644484..119646824,2	K562	blood:
2	chr3:119640550..119642915-chr3:119645017..119647596,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10433404	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10934500	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10934502	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10934503	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10934505	0.84[ASN][1000 genomes]
rs10934506	0.84[ASN][1000 genomes]
rs10934507	0.84[ASN][1000 genomes]
rs11915717	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11917714	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12054090	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12108149	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12629015	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12630829	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12634476	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12634889	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12635018	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12638973	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1574154	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16830567	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1870931	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2276707	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2873950	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28831519	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3814057	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3814058	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4340737	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4624596	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4688042	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688046	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4688047	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4688053	0.82[EUR][1000 genomes]
rs4688054	0.85[ASN][1000 genomes]
rs4688059	0.83[ASN][1000 genomes]
rs56728675	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57939147	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58493895	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58863896	0.81[ASN][1000 genomes]
rs60235167	0.81[ASN][1000 genomes]
rs60389731	0.91[AMR][1000 genomes]
rs60393216	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62264706	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62264708	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62264714	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62264734	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62264739	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62264742	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62264743	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62264747	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62264749	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62266274	0.84[ASN][1000 genomes]
rs62266277	0.81[ASN][1000 genomes]
rs62266281	0.83[ASN][1000 genomes]
rs6773751	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6797459	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6808874	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7633279	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7639388	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119597600-119659000	Weak transcription	Gastric	stomach
3	chr3:119608000-119643600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:119611200-119643400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:119611200-119667000	Weak transcription	Pancreas	Pancrea
7	chr3:119611400-119642000	Weak transcription	Fetal Brain Male	brain
8	chr3:119611400-119649400	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:119611400-119682200	Weak transcription	HSMMtube	muscle
10	chr3:119614200-119645200	Weak transcription	K562	blood
11	chr3:119624600-119642200	Weak transcription	Brain Germinal Matrix	brain
12	chr3:119625000-119668200	Weak transcription	Hela-S3	cervix
13	chr3:119628200-119643000	Weak transcription	Ovary	ovary
14	chr3:119628200-119643800	Weak transcription	Left Ventricle	heart
15	chr3:119628200-119655600	Weak transcription	Fetal Heart	heart
16	chr3:119628200-119663200	Weak transcription	Right Atrium	heart
17	chr3:119628400-119651000	Weak transcription	Right Ventricle	heart
18	chr3:119629600-119672200	Weak transcription	Fetal Stomach	stomach
19	chr3:119630200-119645400	Weak transcription	HUVEC	blood vessel
20	chr3:119630800-119663200	Weak transcription	Esophagus	oesophagus
21	chr3:119630800-119697400	Weak transcription	Thymus	Thymus
22	chr3:119631000-119642800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:119631000-119644000	Weak transcription	Psoas Muscle	Psoas
24	chr3:119631000-119717000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr3:119631200-119647800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:119631200-119650400	Weak transcription	Small Intestine	intestine
27	chr3:119631400-119642800	Weak transcription	Liver	Liver
28	chr3:119631400-119643000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:119631400-119643200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:119631400-119644000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:119631400-119646200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:119631400-119660800	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:119631600-119641600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:119631600-119656000	Weak transcription	NHEK	skin
35	chr3:119631800-119643000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:119632200-119645400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:119633000-119643000	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:119633400-119655600	Weak transcription	Fetal Kidney	kidney
39	chr3:119634000-119656200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr3:119634800-119641800	Weak transcription	NH-A	brain
41	chr3:119635000-119649400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:119635000-119652000	Weak transcription	Adipose Nuclei	Adipose
43	chr3:119635000-119665400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr3:119635000-119667000	Weak transcription	Placenta	Placenta
45	chr3:119635400-119664600	Weak transcription	HMEC	breast
46	chr3:119636200-119645400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:119636400-119667200	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr3:119638600-119641800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr3:119638600-119642800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr3:119638800-119643000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links