Variant report

Variant	rs1228475
Chromosome Location	chr1:223974557-223974558
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1003061	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1153928	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1153937	0.87[ASN][1000 genomes]
rs1153938	0.86[ASN][1000 genomes]
rs1153943	0.85[ASN][1000 genomes]
rs1153944	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1153946	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1153950	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1153952	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1153954	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1153956	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1222081	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1222123	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1222126	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1222127	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1222147	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1222148	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1222153	0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1222158	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1538140	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17739	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1982611	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60739082	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6604726	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6658724	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6661816	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6667215	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6694471	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6698919	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs898878	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223956600-224004600	Strong transcription	Primary monocytes fromperipheralblood	blood
2	chr1:223956600-224004600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:223957000-223983400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:223959800-223977600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:223960200-223998600	Strong transcription	Fetal Thymus	thymus
6	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:223960600-223986800	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr1:223960600-223995200	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:223960600-224001400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:223960800-223995400	Weak transcription	GM12878-XiMat	blood
11	chr1:223961800-223977200	Strong transcription	Duodenum Mucosa	Duodenum
12	chr1:223961800-224004400	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:223962000-223975000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:223962600-223983600	Weak transcription	Psoas Muscle	Psoas
15	chr1:223963400-223983800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr1:223964000-223985600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:223964200-223980000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr1:223964400-223977200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:223964400-223979600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:223964400-224008000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr1:223964600-223976800	Weak transcription	Stomach Mucosa	stomach
22	chr1:223964600-223977000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:223965400-223977200	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr1:223965400-223983800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:223966400-223976200	Weak transcription	NHEK	skin
26	chr1:223966600-223983600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr1:223967800-223979800	Weak transcription	Fetal Brain Male	brain
28	chr1:223968400-223979800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr1:223968400-223984000	Weak transcription	Colonic Mucosa	Colon
30	chr1:223968600-223983000	Weak transcription	Small Intestine	intestine
31	chr1:223968800-223976000	Weak transcription	Hela-S3	cervix
32	chr1:223969000-223983400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:223969200-223975400	Weak transcription	Brain Germinal Matrix	brain
34	chr1:223969200-223983400	Weak transcription	HepG2	liver
35	chr1:223969800-223995200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:223970000-223975000	Strong transcription	Fetal Brain Female	brain
37	chr1:223970000-223995200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:223970200-223977400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:223970200-223977400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:223970400-223975800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:223970600-223976200	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:223970600-223982000	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:223970600-223990400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:223971200-223979600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr1:223971200-223983400	Weak transcription	Esophagus	oesophagus
46	chr1:223971400-223974800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr1:223971400-223976600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr1:223971400-223983400	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:223971400-223985200	Weak transcription	Gastric	stomach
50	chr1:223971400-223985800	Weak transcription	Aorta	Aorta

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