Variant report

Variant	rs2564946
Chromosome Location	chr3:53045290-53045291
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 147 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10049313	1.00[EUR][1000 genomes]
rs1052728	1.00[EUR][1000 genomes]
rs12486028	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12633559	1.00[AMR][1000 genomes]
rs13064076	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13066997	1.00[EUR][1000 genomes]
rs1986738	1.00[EUR][1000 genomes]
rs1986739	1.00[EUR][1000 genomes]
rs1991567	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2001733	1.00[EUR][1000 genomes]
rs2001734	1.00[EUR][1000 genomes]
rs2245536	1.00[EUR][1000 genomes]
rs2246888	1.00[EUR][1000 genomes]
rs2246889	1.00[EUR][1000 genomes]
rs2256728	1.00[EUR][1000 genomes]
rs2256734	1.00[EUR][1000 genomes]
rs2276814	1.00[EUR][1000 genomes]
rs2276819	1.00[EUR][1000 genomes]
rs2276821	1.00[EUR][1000 genomes]
rs2336155	1.00[EUR][1000 genomes]
rs2336157	1.00[EUR][1000 genomes]
rs2336158	1.00[EUR][1000 genomes]
rs2336159	1.00[EUR][1000 genomes]
rs2336161	1.00[EUR][1000 genomes]
rs2336556	1.00[EUR][1000 genomes]
rs2336557	1.00[EUR][1000 genomes]
rs2336559	1.00[EUR][1000 genomes]
rs2535615	1.00[EUR][1000 genomes]
rs2535616	1.00[EUR][1000 genomes]
rs2535618	1.00[EUR][1000 genomes]
rs2535619	1.00[EUR][1000 genomes]
rs2535620	1.00[EUR][1000 genomes]
rs2535621	1.00[EUR][1000 genomes]
rs2535622	1.00[EUR][1000 genomes]
rs2535623	1.00[EUR][1000 genomes]
rs2535624	1.00[EUR][1000 genomes]
rs2535626	1.00[EUR][1000 genomes]
rs2535628	1.00[EUR][1000 genomes]
rs2535631	1.00[EUR][1000 genomes]
rs2535632	1.00[EUR][1000 genomes]
rs2535636	1.00[EUR][1000 genomes]
rs2535637	1.00[EUR][1000 genomes]
rs2535638	1.00[EUR][1000 genomes]
rs2535639	1.00[EUR][1000 genomes]
rs2535641	1.00[EUR][1000 genomes]
rs2535642	1.00[EUR][1000 genomes]
rs2535645	1.00[EUR][1000 genomes]
rs2535646	1.00[EUR][1000 genomes]
rs2564925	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2564927	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2564943	1.00[EUR][1000 genomes]
rs2581781	1.00[AMR][1000 genomes]
rs2581814	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710315	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710316	1.00[EUR][1000 genomes]
rs2710317	1.00[YRI][hapmap]
rs2710318	1.00[EUR][1000 genomes]
rs2710319	1.00[EUR][1000 genomes]
rs2710320	1.00[EUR][1000 genomes]
rs2710321	1.00[EUR][1000 genomes]
rs2710324	1.00[EUR][1000 genomes]
rs2710325	1.00[EUR][1000 genomes]
rs2710327	1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710328	1.00[EUR][1000 genomes]
rs2710329	1.00[EUR][1000 genomes]
rs2710336	1.00[EUR][1000 genomes]
rs2710340	1.00[EUR][1000 genomes]
rs2710343	1.00[EUR][1000 genomes]
rs2710344	1.00[EUR][1000 genomes]
rs2878633	1.00[EUR][1000 genomes]
rs2878634	1.00[EUR][1000 genomes]
rs2878635	1.00[EUR][1000 genomes]
rs2878636	1.00[EUR][1000 genomes]
rs3774361	1.00[EUR][1000 genomes]
rs4234637	1.00[EUR][1000 genomes]
rs4234640	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4687555	1.00[EUR][1000 genomes]
rs4687557	1.00[EUR][1000 genomes]
rs4687558	1.00[YRI][hapmap]
rs4687659	1.00[EUR][1000 genomes]
rs4687661	1.00[EUR][1000 genomes]
rs4687665	1.00[EUR][1000 genomes]
rs4687666	1.00[EUR][1000 genomes]
rs4687667	1.00[EUR][1000 genomes]
rs4687668	1.00[EUR][1000 genomes]
rs4687669	1.00[EUR][1000 genomes]
rs4687670	1.00[EUR][1000 genomes]
rs4687671	1.00[EUR][1000 genomes]
rs4687674	1.00[EUR][1000 genomes]
rs4687675	1.00[EUR][1000 genomes]
rs4687685	1.00[EUR][1000 genomes]
rs4687690	1.00[EUR][1000 genomes]
rs55654539	1.00[AMR][1000 genomes]
rs57430179	1.00[EUR][1000 genomes]
rs58561805	1.00[AMR][1000 genomes]
rs59094265	1.00[EUR][1000 genomes]
rs59234300	1.00[AMR][1000 genomes]
rs61274383	1.00[EUR][1000 genomes]
rs61641433	1.00[EUR][1000 genomes]
rs6445537	1.00[EUR][1000 genomes]
rs6445540	1.00[EUR][1000 genomes]
rs6445542	1.00[EUR][1000 genomes]
rs6445548	1.00[EUR][1000 genomes]
rs6774869	1.00[EUR][1000 genomes]
rs6776862	1.00[EUR][1000 genomes]
rs6776990	1.00[EUR][1000 genomes]
rs6787916	1.00[EUR][1000 genomes]
rs6795138	1.00[EUR][1000 genomes]
rs6797070	1.00[EUR][1000 genomes]
rs72961745	1.00[EUR][1000 genomes]
rs72961755	1.00[EUR][1000 genomes]
rs72967404	1.00[EUR][1000 genomes]
rs72967414	1.00[AMR][1000 genomes]
rs7623667	1.00[EUR][1000 genomes]
rs7629350	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7629528	1.00[EUR][1000 genomes]
rs7637212	1.00[EUR][1000 genomes]
rs7647534	1.00[EUR][1000 genomes]
rs7649515	1.00[EUR][1000 genomes]
rs7650966	1.00[EUR][1000 genomes]
rs7652175	1.00[EUR][1000 genomes]
rs7652476	1.00[EUR][1000 genomes]
rs9681089	1.00[EUR][1000 genomes]
rs9682449	1.00[EUR][1000 genomes]
rs9682819	1.00[EUR][1000 genomes]
rs9815408	1.00[EUR][1000 genomes]
rs9833487	1.00[EUR][1000 genomes]
rs9846827	1.00[EUR][1000 genomes]
rs9869545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9877711	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv3823	chr3:53003659-53051063	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2763768	chr3:53023211-53045925	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv876799	chr3:53024216-53060637	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv517046	chr3:53026714-53046216	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv437713	chr3:53026714-53055522	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv590319	chr3:53027983-53046216	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv590320	chr3:53027983-53055842	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv590321	chr3:53027983-53062661	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv997853	chr3:53028375-53045913	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv590328	chr3:53028375-53046216	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1000857	chr3:53031724-53045913	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1000733	chr3:53031724-53053645	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
15	nsv999029	chr3:53032013-53045913	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv590339	chr3:53033295-53046216	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53019000-53057200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:53019600-53056400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:53020600-53057000	Weak transcription	Dnd41	blood
4	chr3:53022600-53050400	Weak transcription	Primary B cells from cord blood	blood
5	chr3:53025600-53061600	Weak transcription	Lung	lung
6	chr3:53027600-53061600	Weak transcription	Liver	Liver
7	chr3:53027800-53051000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:53030200-53059400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:53030400-53052400	Weak transcription	Primary T cells from cord blood	blood
10	chr3:53030800-53050400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:53032800-53051600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:53033000-53078400	Weak transcription	Aorta	Aorta
13	chr3:53033200-53057000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:53033600-53056200	Weak transcription	Fetal Stomach	stomach
15	chr3:53033800-53052800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:53033800-53053800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:53033800-53060400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:53033800-53065000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr3:53037000-53065000	Weak transcription	Fetal Intestine Small	intestine
20	chr3:53040800-53065000	Weak transcription	Fetal Intestine Large	intestine
21	chr3:53041400-53053600	Weak transcription	Fetal Thymus	thymus
22	chr3:53043000-53046000	Enhancers	GM12878-XiMat	blood
23	chr3:53043200-53045600	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr3:53043600-53045800	Enhancers	HepG2	liver
25	chr3:53043800-53064800	Weak transcription	Stomach Mucosa	stomach
26	chr3:53044000-53045400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:53044000-53045400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr3:53044000-53045600	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr3:53044000-53045800	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr3:53044200-53045400	Enhancers	Adipose Nuclei	Adipose
31	chr3:53044200-53045400	Enhancers	Fetal Muscle Trunk	muscle
32	chr3:53044200-53045400	Enhancers	Psoas Muscle	Psoas
33	chr3:53044200-53045600	Enhancers	Left Ventricle	heart
34	chr3:53044200-53046000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:53044200-53046400	Enhancers	Right Atrium	heart
36	chr3:53044400-53050400	Weak transcription	A549	lung
37	chr3:53044400-53052400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:53044400-53056000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:53044600-53048800	Weak transcription	Pancreas	Pancrea
40	chr3:53044600-53050200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:53044600-53051200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:53044600-53055600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr3:53044600-53065000	Weak transcription	Gastric	stomach
44	chr3:53044800-53045600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr3:53045000-53045600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr3:53045000-53046000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr3:53045000-53050400	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:53045200-53045400	Enhancers	H9 Cell Line	embryonic stem cell
49	chr3:53045200-53045400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr3:53045200-53046000	Enhancers	Rectal Mucosa Donor 31	rectum

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