Variant report

Variant	rs2456828
Chromosome Location	chr1:212898860-212898861
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1021994	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1032963	0.80[ASN][1000 genomes]
rs1032965	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10779583	0.86[ASN][1000 genomes]
rs10864002	0.81[ASN][1000 genomes]
rs11120028	0.89[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11120034	0.81[ASN][1000 genomes]
rs12038225	0.89[AFR][1000 genomes]
rs12568552	0.88[ASN][1000 genomes]
rs12744555	0.81[ASN][1000 genomes]
rs12757944	0.81[ASN][1000 genomes]
rs1813705	0.85[ASN][1000 genomes]
rs2456818	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2456827	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2492779	0.83[AFR][1000 genomes]
rs2492784	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3738800	0.94[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4951464	0.82[ASN][1000 genomes]
rs4951639	0.88[ASN][1000 genomes]
rs6540766	0.88[ASN][1000 genomes]
rs6540767	0.81[ASN][1000 genomes]
rs7528303	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
2	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
3	nsv549148	chr1:212876902-212962207	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2456828	FLVCR1-AS1	cis	Whole Blood	GTEx
rs2456828	LQK1	Cis_1M	lymphoblastoid	RTeQTL
rs2456828	NSL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212895200-212922800	Weak transcription	Left Ventricle	heart
2	chr1:212895400-212899800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:212895400-212901800	Weak transcription	Liver	Liver
4	chr1:212895400-212902000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:212895400-212902400	Weak transcription	Primary T cells from cord blood	blood
6	chr1:212895400-212906000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:212895400-212906600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:212895400-212912000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr1:212895400-212914600	Weak transcription	Spleen	Spleen
10	chr1:212895400-212916600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:212895400-212917400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr1:212895400-212923200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:212895400-212923400	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:212895400-212923400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr1:212895400-212926400	Weak transcription	Esophagus	oesophagus
16	chr1:212895400-212964600	Weak transcription	Pancreas	Pancrea
17	chr1:212895600-212899800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr1:212895600-212900000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:212895600-212900400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr1:212895600-212900400	Weak transcription	Osteobl	bone
21	chr1:212895600-212900600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:212895600-212900600	Weak transcription	NH-A	brain
23	chr1:212895600-212901000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr1:212895600-212904000	Weak transcription	GM12878-XiMat	blood
25	chr1:212895600-212905600	Weak transcription	Lung	lung
26	chr1:212895600-212923000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr1:212895600-212923400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:212895600-212964600	Weak transcription	Gastric	stomach
29	chr1:212895800-212900200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:212895800-212900600	Weak transcription	NHDF-Ad	bronchial
31	chr1:212895800-212901400	Weak transcription	Stomach Mucosa	stomach
32	chr1:212895800-212911200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:212895800-212917400	Weak transcription	NHLF	lung
34	chr1:212895800-212925600	Weak transcription	Small Intestine	intestine
35	chr1:212895800-212926200	Weak transcription	Hela-S3	cervix
36	chr1:212896000-212900800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:212896000-212911800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:212896000-212917000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:212896200-212899800	Weak transcription	Fetal Stomach	stomach
40	chr1:212896200-212900400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:212896200-212901400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr1:212896200-212902200	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:212896200-212906000	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr1:212896200-212908200	Weak transcription	K562	blood
45	chr1:212896200-212912200	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:212896400-212906000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr1:212896400-212917000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:212896800-212909000	Weak transcription	Primary B cells from cord blood	blood
49	chr1:212897200-212899600	Weak transcription	Dnd41	blood
50	chr1:212897200-212899800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links