Variant report

Variant	rs549088
Chromosome Location	chr1:184787131-184787132
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12124929	0.82[ASW][hapmap]
rs12131285	0.82[ASW][hapmap]
rs12567225	0.82[ASW][hapmap]
rs12567226	0.82[ASW][hapmap]
rs1827986	0.88[EUR][1000 genomes]
rs2333715	0.82[ASW][hapmap]
rs338561	0.87[EUR][1000 genomes]
rs338563	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs338564	1.00[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs338565	1.00[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs338567	1.00[CEU][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs338568	1.00[CEU][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes]
rs338571	0.89[EUR][1000 genomes]
rs338572	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs481215	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484847	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs512642	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs520605	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[ASN][1000 genomes]
rs521366	0.93[ASN][1000 genomes]
rs533853	0.91[ASN][1000 genomes]
rs539362	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs543912	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs556163	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs595769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs641337	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001323	chr1:184525419-185315876	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv535222	chr1:184525419-185315876	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv917126	chr1:184655366-184902273	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv832048	chr1:184660146-184858802	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv508677	chr1:184778620-184825302	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv3832	chr1:184784442-184792671	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:184756800-184794000	Weak transcription	Thymus	Thymus
2	chr1:184762000-184787800	Weak transcription	Spleen	Spleen
3	chr1:184762400-184789400	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:184762600-184792800	Weak transcription	Colonic Mucosa	Colon
5	chr1:184768000-184809200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:184772000-184792000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:184772400-184801800	Weak transcription	Primary T cells from cord blood	blood
8	chr1:184772800-184790600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr1:184773200-184809400	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:184775200-184787400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:184775400-184787800	Weak transcription	Esophagus	oesophagus
12	chr1:184775400-184791600	Weak transcription	Stomach Mucosa	stomach
13	chr1:184775600-184796800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr1:184775800-184794000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr1:184777000-184792200	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:184777400-184791600	Weak transcription	Pancreas	Pancrea
17	chr1:184777600-184787600	Weak transcription	Lung	lung
18	chr1:184777800-184787600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:184778000-184787600	Weak transcription	Aorta	Aorta
20	chr1:184778000-184789400	Weak transcription	K562	blood
21	chr1:184778000-184791400	Strong transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:184778200-184787200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:184780400-184787400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr1:184780400-184787600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr1:184780400-184789400	Weak transcription	Fetal Stomach	stomach
26	chr1:184781200-184793400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:184781400-184790000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:184781400-184792000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr1:184781600-184790800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:184781600-184793400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:184782000-184789800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr1:184783000-184787600	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:184783000-184807800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:184783200-184787600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr1:184783200-184788600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr1:184783200-184789400	Weak transcription	NHEK	skin
37	chr1:184783200-184789600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:184783200-184791200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:184783200-184791200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:184783200-184796400	Weak transcription	NHLF	lung
41	chr1:184783200-184796800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:184783200-184796800	Weak transcription	NHDF-Ad	bronchial
43	chr1:184783200-184809200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr1:184783400-184788400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:184783400-184803200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:184784000-184787600	Weak transcription	GM12878-XiMat	blood
47	chr1:184784000-184789400	Strong transcription	Left Ventricle	heart
48	chr1:184784000-184793200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:184784200-184789600	Strong transcription	Fetal Heart	heart
50	chr1:184784200-184794000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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