Variant report

Variant	rs2465148
Chromosome Location	chr12:86658734-86658735
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10776953	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10776954	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10776958	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10776960	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10776967	0.95[EUR][1000 genomes]
rs10858409	0.90[EUR][1000 genomes]
rs10858411	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10858417	0.94[EUR][1000 genomes]
rs10858420	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11103946	0.93[EUR][1000 genomes]
rs1389292	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1389294	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1389295	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1463749	0.92[ASN][1000 genomes]
rs1493408	0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1493413	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1493414	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1493416	0.92[ASN][1000 genomes]
rs1493417	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1493418	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1493420	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1493421	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1532263	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1552839	0.80[ASN][1000 genomes]
rs1602850	0.92[ASN][1000 genomes]
rs1994863	0.85[EUR][1000 genomes]
rs2131565	0.80[ASN][1000 genomes]
rs2250915	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2406120	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2406121	0.96[EUR][1000 genomes]
rs2452803	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2452805	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2452806	0.92[ASN][1000 genomes]
rs2452808	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2452811	0.80[ASN][1000 genomes]
rs2452815	0.80[ASN][1000 genomes]
rs2465142	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2465145	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2465146	0.92[ASN][1000 genomes]
rs2471561	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2471562	0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2471563	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2471567	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4329741	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7137308	0.92[ASN][1000 genomes]
rs7303642	0.96[EUR][1000 genomes]
rs7953494	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7954833	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7963957	0.90[EUR][1000 genomes]
rs7966656	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs839107	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049179	chr12:86056376-86799188	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2761759	chr12:86415936-86747726	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv518059	chr12:86416212-86747726	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1041397	chr12:86438607-86737558	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1053087	chr12:86569126-86733418	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv541564	chr12:86569126-86733418	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1037003	chr12:86610040-86798121	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1045386	chr12:86616015-86733418	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv541565	chr12:86616015-86733418	Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:86657800-86659200	Enhancers	Fetal Heart	heart
2	chr12:86658000-86659200	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr12:86658000-86659200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:86658000-86659200	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr12:86658000-86659200	Active TSS	Colonic Mucosa	Colon
6	chr12:86658000-86659400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:86658000-86659600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr12:86658200-86658800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:86658200-86658800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:86658200-86658800	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr12:86658200-86658800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr12:86658200-86658800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:86658200-86658800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
14	chr12:86658200-86658800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
15	chr12:86658200-86658800	Active TSS	Fetal Intestine Small	intestine
16	chr12:86658200-86659000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr12:86658200-86659000	Active TSS	H9 Cell Line	embryonic stem cell
18	chr12:86658200-86659000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr12:86658200-86659000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr12:86658200-86659000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:86658200-86659000	Active TSS	Duodenum Mucosa	Duodenum
22	chr12:86658200-86659000	Active TSS	Fetal Brain Female	brain
23	chr12:86658200-86659000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr12:86658200-86659000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
25	chr12:86658200-86659000	Flanking Active TSS	Placenta Amnion	Placenta Amnion
26	chr12:86658200-86659000	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr12:86658200-86659000	Active TSS	Right Atrium	heart
28	chr12:86658200-86659000	Active TSS	HepG2	liver
29	chr12:86658200-86659200	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr12:86658200-86659200	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr12:86658200-86659200	Active TSS	Brain Angular Gyrus	brain
32	chr12:86658200-86659200	Active TSS	Brain Substantia Nigra	brain
33	chr12:86658200-86659200	Active TSS	Gastric	stomach
34	chr12:86658200-86659200	Flanking Active TSS	Pancreas	Pancrea
35	chr12:86658200-86659200	Active TSS	Right Ventricle	heart
36	chr12:86658400-86658800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr12:86658400-86658800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:86658400-86659000	Active TSS	Brain Cingulate Gyrus	brain
39	chr12:86658400-86659000	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr12:86658400-86659000	Active TSS	Fetal Lung	lung
41	chr12:86658400-86659000	Active TSS	Stomach Mucosa	stomach
42	chr12:86658400-86659200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:86658400-86659200	Active TSS	Brain Germinal Matrix	brain
44	chr12:86658400-86659200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr12:86658400-86659200	Active TSS	Rectal Smooth Muscle	rectum
46	chr12:86658400-86659200	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr12:86658400-86659400	Active TSS	Fetal Kidney	kidney
48	chr12:86658400-86659400	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr12:86658600-86658800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:86658600-86658800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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