Variant report

Variant	rs9880050
Chromosome Location	chr3:51724147-51724148
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs12330534	1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13314120	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13321674	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13325153	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.95[YRI][hapmap]
rs13327225	1.00[MEX][hapmap]
rs13433729	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17051799	0.85[AMR][1000 genomes]
rs17051832	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17081501	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28421789	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28452990	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28457212	0.85[AMR][1000 genomes]
rs28653367	0.85[AMR][1000 genomes]
rs2883900	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549265	0.85[AMR][1000 genomes]
rs56942057	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59064710	1.00[ASN][1000 genomes]
rs59525691	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60823123	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61440245	1.00[ASN][1000 genomes]
rs61737032	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6792143	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs6806124	1.00[MEX][hapmap]
rs72951441	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951452	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951472	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951485	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72951486	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953413	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953417	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953419	1.00[ASN][1000 genomes]
rs72953421	1.00[ASN][1000 genomes]
rs72953423	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72953429	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7627636	1.00[ASN][1000 genomes]
rs904144	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9311470	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9808940	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9809757	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812008	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9812682	1.00[ASN][1000 genomes]
rs9815475	1.00[MEX][hapmap]
rs9815684	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9816075	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824779	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826664	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9827665	0.85[AMR][1000 genomes]
rs9827917	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838294	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838942	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9838994	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839516	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9839608	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9842066	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9844541	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9846343	1.00[ASN][1000 genomes]
rs9855809	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9857893	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9864952	1.00[ASN][1000 genomes]
rs9866513	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9866604	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9870147	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9875460	0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9878564	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs9880909	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881402	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9881844	0.85[AMR][1000 genomes]
rs9882601	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9990341	0.85[AMR][1000 genomes];1.00[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	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
2	esv1814919	chr3:51703488-51752684	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv590278	chr3:51724147-51736744	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv590279	chr3:51724147-51737852	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51706400-51733400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:51706400-51741000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:51706600-51724600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr3:51706600-51739600	Weak transcription	Small Intestine	intestine
5	chr3:51707800-51740400	Strong transcription	Fetal Intestine Small	intestine
6	chr3:51708800-51738800	Strong transcription	Fetal Intestine Large	intestine
7	chr3:51716200-51726200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:51716200-51737000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:51716400-51741200	Weak transcription	Fetal Kidney	kidney
10	chr3:51716600-51724800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:51716800-51726600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:51716800-51738800	Strong transcription	Cortex derived primary cultured neurospheres	brain
13	chr3:51717000-51727400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:51717400-51739800	Strong transcription	Liver	Liver
15	chr3:51717800-51725200	Strong transcription	Gastric	stomach
16	chr3:51718000-51726800	Strong transcription	Pancreas	Pancrea
17	chr3:51719600-51726000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr3:51719600-51741200	Weak transcription	NHDF-Ad	bronchial
19	chr3:51719800-51732400	Weak transcription	Hela-S3	cervix
20	chr3:51720000-51733200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:51720200-51733000	Weak transcription	Fetal Lung	lung
22	chr3:51720400-51727200	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:51720600-51739800	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr3:51720600-51740000	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:51721000-51724600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:51721000-51735600	Weak transcription	K562	blood
27	chr3:51721000-51738200	Weak transcription	A549	lung
28	chr3:51721000-51741000	Weak transcription	HUVEC	blood vessel
29	chr3:51721200-51724200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:51721200-51724200	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr3:51721200-51724200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr3:51721200-51724400	Strong transcription	Brain Hippocampus Middle	brain
33	chr3:51721400-51724400	Strong transcription	GM12878-XiMat	blood
34	chr3:51721400-51734200	Genic enhancers	Primary T cells fromperipheralblood	blood
35	chr3:51721400-51738800	Strong transcription	Colonic Mucosa	Colon
36	chr3:51721400-51739400	Strong transcription	Thymus	Thymus
37	chr3:51721400-51739800	Strong transcription	Duodenum Mucosa	Duodenum
38	chr3:51721400-51740000	Strong transcription	Placenta	Placenta
39	chr3:51721400-51740200	Strong transcription	Esophagus	oesophagus
40	chr3:51721400-51740400	Strong transcription	Dnd41	blood
41	chr3:51721400-51740600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr3:51721400-51740800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:51721600-51724200	Strong transcription	Brain Anterior Caudate	brain
44	chr3:51721600-51725000	Strong transcription	Lung	lung
45	chr3:51721600-51725200	Weak transcription	Fetal Brain Female	brain
46	chr3:51721600-51725400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr3:51721600-51726200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:51721600-51727600	Strong transcription	Ovary	ovary
49	chr3:51721600-51739400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr3:51721600-51740400	Strong transcription	Fetal Stomach	stomach

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