Variant report

Variant	rs6006090
Chromosome Location	chr22:29705927-29705928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11090564	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs131180	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs131182	0.89[ASN][1000 genomes]
rs131189	0.89[ASN][1000 genomes]
rs140062	1.00[CHB][hapmap];0.94[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140063	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140066	0.94[ASN][1000 genomes]
rs174759	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs174761	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs174762	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs174764	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs174765	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs174766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs174767	0.83[ASN][1000 genomes]
rs174769	0.89[ASN][1000 genomes]
rs174770	0.88[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs174771	0.89[ASN][1000 genomes]
rs2071578	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2072051	0.88[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2267132	0.82[CHB][hapmap];0.84[JPT][hapmap]
rs2267133	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs2283849	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2283850	0.88[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2301290	1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2301291	0.80[JPT][hapmap]
rs2301585	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2519486	0.85[ASN][1000 genomes]
rs2857462	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2857466	0.89[JPT][hapmap]
rs28755	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3788410	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3788411	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4820803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4820804	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5752903	0.88[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs5763138	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5763139	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5763178	0.89[ASN][1000 genomes]
rs6006098	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs715494	0.88[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs737883	0.80[JPT][hapmap]
rs762817	0.82[ASN][1000 genomes]
rs879580	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs909798	0.84[JPT][hapmap]
rs9537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs98069	1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv829154	chr22:29617485-29724001	Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv834171	chr22:29626402-29829844	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv829155	chr22:29664396-29724001	Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv529742	chr22:29677909-30274388	Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv914959	chr22:29696438-29712874	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv914960	chr22:29696438-29714069	Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29702000-29707800	Enhancers	Fetal Heart	heart
2	chr22:29702800-29706400	Weak transcription	GM12878-XiMat	blood
3	chr22:29703000-29706400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr22:29703200-29707600	Enhancers	Fetal Brain Male	brain
5	chr22:29703600-29706000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr22:29703600-29706000	Flanking Active TSS	Duodenum Mucosa	Duodenum
7	chr22:29703600-29706000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
8	chr22:29703600-29706000	Flanking Active TSS	Hela-S3	cervix
9	chr22:29703600-29706800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr22:29703600-29707600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr22:29703600-29707800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr22:29703600-29708000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr22:29703800-29706800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:29703800-29706800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr22:29703800-29706800	Weak transcription	Aorta	Aorta
16	chr22:29703800-29707000	Genic enhancers	Fetal Intestine Small	intestine
17	chr22:29703800-29707000	Enhancers	Small Intestine	intestine
18	chr22:29703800-29707600	Enhancers	Fetal Intestine Large	intestine
19	chr22:29703800-29708000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr22:29703800-29708400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr22:29703800-29709400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr22:29704000-29706000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr22:29704000-29706000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr22:29704000-29706000	Flanking Active TSS	HSMM	muscle
25	chr22:29704000-29706600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr22:29704000-29706600	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr22:29704000-29706600	Genic enhancers	Fetal Stomach	stomach
28	chr22:29704000-29707600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr22:29704000-29707800	Enhancers	Ovary	ovary
30	chr22:29704000-29709600	Enhancers	Placenta	Placenta
31	chr22:29704200-29706000	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr22:29704200-29708800	Genic enhancers	Fetal Muscle Leg	muscle
33	chr22:29704400-29706800	Enhancers	A549	lung
34	chr22:29704400-29707400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
35	chr22:29704400-29707800	Enhancers	Lung	lung
36	chr22:29704400-29708000	Enhancers	Pancreas	Pancrea
37	chr22:29704400-29708600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr22:29704600-29706600	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr22:29704600-29707600	Enhancers	Spleen	Spleen
40	chr22:29704600-29707800	Enhancers	Gastric	stomach
41	chr22:29704600-29708000	Genic enhancers	NHLF	lung
42	chr22:29704800-29706000	Flanking Active TSS	Colonic Mucosa	Colon
43	chr22:29704800-29706400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr22:29704800-29706800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr22:29705000-29706000	Flanking Active TSS	Stomach Smooth Muscle	stomach
46	chr22:29705000-29706000	Flanking Active TSS	HUVEC	blood vessel
47	chr22:29705000-29706200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr22:29705200-29706400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr22:29705200-29706400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr22:29705200-29706400	Weak transcription	Brain Substantia Nigra	brain

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