Variant report

Variant	rs9880909
Chromosome Location	chr3:51511737-51511738
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs12330534	1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12493978	0.94[YRI][hapmap]
rs13314120	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13316894	1.00[MEX][hapmap]
rs13321674	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13325153	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.94[YRI][hapmap]
rs13433729	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1480366	1.00[ASW][hapmap]
rs17051685	1.00[ASW][hapmap]
rs17051799	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051802	1.00[ASW][hapmap]
rs17051832	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17081501	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1842394	0.87[YRI][hapmap]
rs2170177	1.00[ASW][hapmap]
rs28421789	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28452990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28457212	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28653367	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2883900	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4468966	0.94[YRI][hapmap]
rs4549265	1.00[AMR][1000 genomes]
rs4974112	1.00[ASW][hapmap]
rs56942057	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59064710	1.00[ASN][1000 genomes]
rs59525691	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60823123	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61440245	1.00[ASN][1000 genomes]
rs61737032	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6779163	1.00[MEX][hapmap]
rs6782997	1.00[MEX][hapmap]
rs6806124	1.00[MEX][hapmap]
rs72951441	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951452	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951472	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951485	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951486	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953413	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953417	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953419	1.00[ASN][1000 genomes]
rs72953421	1.00[ASN][1000 genomes]
rs72953423	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953429	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs751076	0.94[YRI][hapmap]
rs7627636	1.00[ASN][1000 genomes]
rs880478	0.94[YRI][hapmap]
rs904144	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9311470	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9808940	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9809757	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812008	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812682	1.00[ASN][1000 genomes]
rs9815684	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9816075	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9817077	0.94[YRI][hapmap]
rs9817872	0.94[YRI][hapmap]
rs9819195	0.94[YRI][hapmap]
rs9824779	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826664	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9827665	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9827917	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9828325	1.00[MEX][hapmap]
rs9829057	0.94[YRI][hapmap]
rs9838294	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838942	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838994	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839516	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839608	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9840331	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9842066	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9844541	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9846343	1.00[ASN][1000 genomes]
rs9855214	1.00[MEX][hapmap]
rs9855809	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9856134	0.88[YRI][hapmap]
rs9857893	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858497	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9864213	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9864952	1.00[ASN][1000 genomes]
rs9866513	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866604	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9870147	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9875460	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9878053	1.00[MEX][hapmap]
rs9880050	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881402	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881844	1.00[AMR][1000 genomes]
rs9882601	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9990341	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014464	chr3:51220151-51909780	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer 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	53 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	chr3:51458200-51515000	Weak transcription	Fetal Brain Male	brain
2	chr3:51467800-51524000	Weak transcription	Small Intestine	intestine
3	chr3:51477200-51515000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr3:51490400-51515000	Weak transcription	Stomach Mucosa	stomach
5	chr3:51491400-51532800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:51495000-51532600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:51495400-51513200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:51495800-51518200	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr3:51495800-51518200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:51495800-51526800	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr3:51495800-51531800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:51496000-51517800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr3:51496000-51518400	Strong transcription	Fetal Stomach	stomach
14	chr3:51496000-51531800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:51496200-51516600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:51496200-51516800	Strong transcription	Dnd41	blood
17	chr3:51496200-51518000	Strong transcription	Placenta	Placenta
18	chr3:51496200-51530600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:51496200-51531000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr3:51496400-51525800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr3:51497200-51524400	Weak transcription	Right Ventricle	heart
22	chr3:51497600-51518200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:51498000-51514000	Weak transcription	Brain Substantia Nigra	brain
24	chr3:51498000-51515000	Weak transcription	Esophagus	oesophagus
25	chr3:51499400-51514600	Weak transcription	NHDF-Ad	bronchial
26	chr3:51499400-51532800	Weak transcription	Fetal Heart	heart
27	chr3:51499600-51517800	Strong transcription	Fetal Intestine Small	intestine
28	chr3:51500600-51532800	Weak transcription	Fetal Kidney	kidney
29	chr3:51500800-51514800	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:51501000-51511800	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:51501000-51514200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr3:51501000-51515000	Weak transcription	A549	lung
33	chr3:51501000-51532400	Weak transcription	Psoas Muscle	Psoas
34	chr3:51501000-51532800	Weak transcription	NH-A	brain
35	chr3:51502200-51512800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:51503400-51512000	Weak transcription	HSMM	muscle
37	chr3:51503400-51514400	Weak transcription	HMEC	breast
38	chr3:51503600-51513200	Weak transcription	Brain Cingulate Gyrus	brain
39	chr3:51503800-51512000	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:51504000-51515400	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr3:51504800-51533000	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:51505000-51531600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr3:51505000-51533000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:51505200-51512000	Weak transcription	Primary neutrophils fromperipheralblood	blood
45	chr3:51505200-51514800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr3:51506400-51512000	Weak transcription	HepG2	liver
47	chr3:51506400-51513200	Weak transcription	Pancreas	Pancrea
48	chr3:51506400-51514600	Weak transcription	NHLF	lung
49	chr3:51506400-51523200	Weak transcription	HSMMtube	muscle
50	chr3:51506600-51511800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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