Variant report

Variant	rs2644248
Chromosome Location	chr15:34587514-34587515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11631094	0.83[ASN][1000 genomes]
rs12591967	0.87[ASN][1000 genomes]
rs12592443	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12594569	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs168335	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16958910	0.85[ASN][1000 genomes]
rs16958954	0.87[ASN][1000 genomes]
rs16958989	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2085966	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2126421	0.85[ASN][1000 genomes]
rs2644245	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2644247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs347804	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs347805	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs347806	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs347807	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs347809	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs347810	0.93[ASN][1000 genomes]
rs347812	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs347813	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs347817	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs347818	0.91[ASN][1000 genomes]
rs347819	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs347822	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs347823	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs347824	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs347842	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs347843	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs347845	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs347846	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs347847	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs347848	0.86[ASN][1000 genomes]
rs347849	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs347851	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs347856	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs347858	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs347860	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs347861	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs347866	0.89[ASN][1000 genomes]
rs347867	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs405080	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs419179	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs426634	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs436552	0.93[ASN][1000 genomes]
rs4387570	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs440025	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs442006	0.93[ASN][1000 genomes]
rs449053	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56207527	0.80[ASN][1000 genomes]
rs56388838	0.81[ASN][1000 genomes]
rs57715165	0.83[ASN][1000 genomes]
rs57875866	0.86[ASN][1000 genomes]
rs59802332	0.90[ASN][1000 genomes]
rs60114685	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60539207	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6495660	0.82[ASN][1000 genomes]
rs7163919	0.86[ASN][1000 genomes]
rs7164902	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7181260	0.81[ASN][1000 genomes]
rs7183269	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73374434	0.83[ASN][1000 genomes]
rs73390084	0.83[ASN][1000 genomes]
rs73392004	0.86[ASN][1000 genomes]
rs7495538	0.86[ASN][1000 genomes]
rs8025057	0.81[ASN][1000 genomes]
rs8041425	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8043005	0.83[ASN][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	nsv1052804	chr15:34498529-34841447	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv542341	chr15:34498529-34841447	Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1045173	chr15:34501055-34596995	Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	esv1798578	chr15:34543021-34988247	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	esv1804312	chr15:34543021-34988247	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	esv1821622	chr15:34543021-34988247	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	esv1850950	chr15:34543021-34988247	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
8	esv2758376	chr15:34543021-34988247	Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
9	esv2760024	chr15:34543021-34988247	Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
10	nsv428303	chr15:34543021-34988247	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv1036475	chr15:34552879-34841587	Bivalent/Poised TSS Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
12	nsv542342	chr15:34552879-34841587	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
13	nsv1048550	chr15:34553078-34841447	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
14	nsv542343	chr15:34553078-34841447	Active TSS Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
15	nsv471682	chr15:34560451-34882630	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
16	nsv1051403	chr15:34573065-34600474	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
17	nsv819906	chr15:34585431-34597560	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2644248	NOP10	cis	Thyroid	GTEx
rs2644248	SLC12A6	cis	Thyroid	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34547600-34591200	Weak transcription	Aorta	Aorta
2	chr15:34548200-34592600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr15:34551200-34608800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:34555200-34606600	Weak transcription	Thymus	Thymus
5	chr15:34577600-34590800	Weak transcription	Primary T cells from cord blood	blood
6	chr15:34577600-34608800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:34577600-34610200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr15:34577800-34589600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr15:34577800-34593200	Weak transcription	HepG2	liver
10	chr15:34577800-34608800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr15:34578000-34589600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr15:34578200-34606800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr15:34579000-34603800	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr15:34582200-34599000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr15:34582600-34609600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr15:34582600-34610200	Weak transcription	Fetal Lung	lung
17	chr15:34583200-34588800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr15:34583400-34588800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:34583400-34609600	Weak transcription	Adipose Nuclei	Adipose
20	chr15:34583600-34593600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:34583800-34610600	Weak transcription	Pancreas	Pancrea
22	chr15:34584600-34587800	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr15:34584600-34588800	Weak transcription	Rectal Smooth Muscle	rectum
24	chr15:34584800-34587600	ZNF genes & repeats	GM12878-XiMat	blood
25	chr15:34584800-34589200	Weak transcription	Colon Smooth Muscle	Colon
26	chr15:34585000-34588800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr15:34585000-34609600	Weak transcription	Spleen	Spleen
28	chr15:34585000-34610600	Weak transcription	Lung	lung
29	chr15:34585200-34588600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr15:34585200-34588800	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr15:34585200-34589600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:34585200-34589600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr15:34585200-34589600	Weak transcription	Left Ventricle	heart
34	chr15:34585200-34596400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr15:34585200-34598600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:34585200-34609600	Weak transcription	Fetal Stomach	stomach
37	chr15:34585200-34615600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:34585400-34589200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr15:34585400-34602200	Weak transcription	Esophagus	oesophagus
40	chr15:34585400-34608600	Weak transcription	Liver	Liver
41	chr15:34585600-34587600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:34585800-34588800	Weak transcription	Hela-S3	cervix
43	chr15:34585800-34590400	Weak transcription	Right Ventricle	heart
44	chr15:34585800-34604600	Weak transcription	Fetal Intestine Large	intestine
45	chr15:34585800-34610400	Weak transcription	Ovary	ovary
46	chr15:34586400-34592800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:34586600-34588800	Weak transcription	Psoas Muscle	Psoas
48	chr15:34586600-34609800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr15:34587000-34610200	Weak transcription	Fetal Intestine Small	intestine
50	chr15:34587200-34587800	Strong transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links