Variant report

Variant	rs11720540
Chromosome Location	chr3:143696161-143696162
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:143695787..143698743-chr3:143748690..143750623,2	K562	blood:
2	chr3:143694108..143696591-chr3:143721286..143722845,2	K562	blood:
3	chr3:143694211..143696611-chr3:143698183..143700521,4	K562	blood:
4	chr3:143695188..143697980-chr3:143701408..143704204,2	MCF-7	breast:
5	chr3:143694586..143698442-chr3:143710768..143713586,3	K562	blood:

Extended variants
information (count: 121 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1027726	0.85[ASN][1000 genomes]
rs1027727	0.85[ASN][1000 genomes]
rs1125704	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1125705	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11710441	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11914522	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13062780	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13083596	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13092757	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13323371	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1354495	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1370027	0.87[ASN][1000 genomes]
rs1370028	0.87[ASN][1000 genomes]
rs1370029	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1370030	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1394399	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1394400	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1394401	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1436629	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1469871	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1504596	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1504601	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1550141	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1550142	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1583550	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1595208	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1595209	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1595210	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1595211	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17603166	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1898263	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1992094	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2118071	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2118072	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2134914	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2134915	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2134916	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2164551	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2217926	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2221411	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2361211	0.88[ASN][1000 genomes]
rs2370174	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2370175	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs34200306	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34743418	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs35291263	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4258964	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4258965	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4276180	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4334641	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4350918	0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4431106	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4437138	0.80[AMR][1000 genomes]
rs4462961	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4476500	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4549268	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4563410	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4575896	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4582058	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59870355	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6440206	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6440207	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6440208	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6440209	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs67417607	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6766439	0.88[ASN][1000 genomes]
rs6767811	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6770317	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6798775	0.87[ASN][1000 genomes]
rs6803148	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs723490	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs723492	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7432451	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7611555	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611648	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7611814	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7619036	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7619220	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7622357	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7626898	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7628282	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7630146	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7631704	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7638577	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7643341	0.85[ASN][1000 genomes]
rs7650233	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7650239	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7650332	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7650459	0.88[ASN][1000 genomes]
rs7651567	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7652490	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7653287	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7653431	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9289671	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9683376	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9811736	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9811888	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9812340	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9812374	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9829883	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9835170	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9840157	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9840519	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9840971	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9841182	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9854844	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9860872	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9865128	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9867025	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9867615	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9867976	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9869178	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9870551	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9872448	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9872595	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9876654	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9878070	0.86[AMR][1000 genomes];0.90[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	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv518814	chr3:143666825-143703750	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	31 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	chr3:143688800-143696400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr3:143689000-143696800	Active TSS	Stomach Smooth Muscle	stomach
3	chr3:143689200-143696200	Active TSS	GM12878-XiMat	blood
4	chr3:143689400-143696200	Active TSS	Brain Angular Gyrus	brain
5	chr3:143689400-143696400	Active TSS	Fetal Brain Female	brain
6	chr3:143689400-143696800	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr3:143689400-143697200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:143689600-143696800	Active TSS	Ovary	ovary
9	chr3:143689800-143696800	Active TSS	HSMMtube	muscle
10	chr3:143692600-143707800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr3:143692800-143714200	Weak transcription	Small Intestine	intestine
12	chr3:143693000-143696200	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr3:143693000-143697800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr3:143693000-143697800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr3:143693400-143697800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
16	chr3:143693400-143699400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr3:143693400-143706800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:143693400-143708400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:143693400-143708400	Weak transcription	Psoas Muscle	Psoas
20	chr3:143693400-143713800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr3:143693600-143696800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:143693600-143698400	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr3:143693600-143711600	Weak transcription	Left Ventricle	heart
24	chr3:143693800-143696600	Enhancers	Rectal Smooth Muscle	rectum
25	chr3:143693800-143696800	Weak transcription	NH-A	brain
26	chr3:143693800-143697200	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr3:143693800-143697800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr3:143693800-143698200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:143693800-143701600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr3:143694000-143696200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:143694000-143696200	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr3:143694000-143697800	Enhancers	Primary T cells from cord blood	blood
33	chr3:143694000-143698400	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr3:143694000-143708000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:143694200-143703200	Weak transcription	Placenta	Placenta
36	chr3:143694200-143705600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:143694400-143696200	Enhancers	Primary B cells from cord blood	blood
38	chr3:143694400-143696200	Weak transcription	Adipose Nuclei	Adipose
39	chr3:143694400-143696400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:143694400-143696400	Weak transcription	Osteobl	bone
41	chr3:143694400-143697200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:143694400-143697200	Enhancers	Liver	Liver
43	chr3:143694400-143700000	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr3:143694400-143708400	Weak transcription	Fetal Intestine Small	intestine
45	chr3:143694400-143718800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr3:143694400-143719400	Weak transcription	Hela-S3	cervix
47	chr3:143694600-143696400	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr3:143694800-143697000	Active TSS	Aorta	Aorta
49	chr3:143694800-143698400	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr3:143694800-143707200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links