Variant report

Variant	rs6006309
Chromosome Location	chr22:30341454-30341455
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs16988115	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16988122	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16988151	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28647168	1.00[AMR][1000 genomes]
rs56733052	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57258477	1.00[AMR][1000 genomes]
rs57724305	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58255360	1.00[AMR][1000 genomes]
rs58952888	0.83[AMR][1000 genomes]
rs59580785	1.00[AMR][1000 genomes]
rs5997540	1.00[AMR][1000 genomes]
rs5997565	1.00[AMR][1000 genomes]
rs6006297	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6006299	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6006301	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6006317	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6006318	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6006331	1.00[AMR][1000 genomes]
rs60245742	1.00[AMR][1000 genomes]
rs60964812	1.00[AMR][1000 genomes]
rs61043203	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61191536	1.00[AMR][1000 genomes]
rs61540772	1.00[AMR][1000 genomes]
rs73394851	1.00[AMR][1000 genomes]
rs73394860	1.00[AMR][1000 genomes]
rs73394861	1.00[AMR][1000 genomes]
rs73394863	1.00[AMR][1000 genomes]
rs73394876	1.00[AMR][1000 genomes]
rs73396842	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73396845	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73398604	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73398634	0.87[AFR][1000 genomes]
rs73398637	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73398640	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73398663	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73400621	0.83[AMR][1000 genomes]
rs73400633	1.00[AMR][1000 genomes]
rs73400648	1.00[AMR][1000 genomes]
rs73400675	1.00[AMR][1000 genomes]
rs73400689	1.00[AMR][1000 genomes]
rs73402619	1.00[AMR][1000 genomes]
rs73402627	1.00[AMR][1000 genomes]
rs73402640	1.00[AMR][1000 genomes]
rs73402644	1.00[AMR][1000 genomes]
rs73402647	1.00[AMR][1000 genomes]
rs73402653	1.00[AMR][1000 genomes]
rs9620939	0.83[AMR][1000 genomes]
rs9625903	0.83[AMR][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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv1064489	chr22:30316627-30361881	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv869764	chr22:30323649-30367813	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv523696	chr22:30326102-30381789	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1058511	chr22:30330447-30361881	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv2763694	chr22:30330459-30361881	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv588883	chr22:30333405-30365842	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30311600-30343800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr22:30313000-30343800	Weak transcription	Fetal Stomach	stomach
3	chr22:30313600-30354200	Weak transcription	Small Intestine	intestine
4	chr22:30327600-30342200	Weak transcription	Brain Angular Gyrus	brain
5	chr22:30328400-30343600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr22:30328400-30351800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr22:30330600-30342200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr22:30332000-30342200	Weak transcription	Gastric	stomach
9	chr22:30332600-30345000	Weak transcription	Pancreas	Pancrea
10	chr22:30332600-30347400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr22:30332800-30343800	Weak transcription	Adipose Nuclei	Adipose
12	chr22:30333600-30343600	Weak transcription	Brain Anterior Caudate	brain
13	chr22:30334200-30374800	Weak transcription	Thymus	Thymus
14	chr22:30337000-30342000	Weak transcription	Brain Substantia Nigra	brain
15	chr22:30339000-30343000	Weak transcription	Brain Germinal Matrix	brain
16	chr22:30339400-30341800	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr22:30339800-30341800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr22:30339800-30342600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr22:30339800-30343200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr22:30340000-30342600	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr22:30340000-30342600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr22:30340000-30344000	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr22:30340000-30344800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr22:30340000-30345000	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr22:30340000-30345000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr22:30340000-30346800	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr22:30340200-30342200	Weak transcription	Spleen	Spleen
28	chr22:30340200-30342600	Enhancers	K562	blood
29	chr22:30340200-30343200	Weak transcription	NHLF	lung
30	chr22:30340200-30344200	Weak transcription	Right Ventricle	heart
31	chr22:30340200-30351000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr22:30340200-30355400	Weak transcription	Fetal Intestine Small	intestine
33	chr22:30340200-30374800	Weak transcription	Fetal Thymus	thymus
34	chr22:30340400-30343000	Enhancers	Colon Smooth Muscle	Colon
35	chr22:30340600-30341600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr22:30340600-30342000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr22:30340600-30342400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr22:30340600-30347400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr22:30340600-30347600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr22:30340600-30347600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr22:30340600-30360400	Weak transcription	Primary hematopoietic stem cells	blood
42	chr22:30340600-30370000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr22:30340600-30375000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr22:30340800-30341600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr22:30340800-30342000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr22:30340800-30342000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr22:30340800-30342000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr22:30340800-30342200	Weak transcription	Fetal Lung	lung
49	chr22:30340800-30342600	Enhancers	Ovary	ovary
50	chr22:30340800-30342800	Weak transcription	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links