Variant report

Variant	rs2857466
Chromosome Location	chr22:29657604-29657605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:95619300..95619800-chr22:29657270..29657935,2	NB4	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11090564	0.89[JPT][hapmap]
rs140062	0.83[JPT][hapmap]
rs174761	0.89[JPT][hapmap]
rs174762	0.83[JPT][hapmap]
rs174764	0.89[JPT][hapmap]
rs174766	0.89[JPT][hapmap]
rs2071578	0.83[JPT][hapmap]
rs2267135	0.89[JPT][hapmap]
rs2283849	0.89[JPT][hapmap]
rs2283852	0.83[JPT][hapmap]
rs2301290	0.84[CHD][hapmap];0.83[JPT][hapmap]
rs2301291	0.80[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2301585	0.89[JPT][hapmap]
rs2301586	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2744465	0.86[MKK][hapmap]
rs3788410	0.89[JPT][hapmap]
rs3788411	0.89[JPT][hapmap]
rs3788412	0.83[JPT][hapmap]
rs4034938	0.88[JPT][hapmap]
rs4820803	0.89[JPT][hapmap]
rs4820804	0.89[JPT][hapmap]
rs5752905	0.80[CHD][hapmap];0.83[JPT][hapmap]
rs5752907	0.83[JPT][hapmap]
rs5763138	0.83[JPT][hapmap]
rs5763139	0.89[JPT][hapmap]
rs5763144	0.80[EUR][1000 genomes]
rs5763171	0.83[JPT][hapmap]
rs5763182	0.83[JPT][hapmap]
rs5763184	0.83[JPT][hapmap]
rs5763190	0.89[JPT][hapmap]
rs6006090	0.89[JPT][hapmap]
rs6006098	0.83[JPT][hapmap]
rs6006108	0.83[JPT][hapmap]
rs6006113	0.83[JPT][hapmap]
rs6006115	0.85[JPT][hapmap]
rs737883	0.85[CHB][hapmap];0.94[JPT][hapmap]
rs879580	0.89[JPT][hapmap]
rs909798	0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9537	0.82[CHD][hapmap];0.89[JPT][hapmap]
rs9613859	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs98069	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv1809952	chr22:29595349-29661434	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers 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	6 gene(s)	inside rSNPs	diseases
3	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
4	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2857466	SMARCB1	cis	cerebellum	SCAN
rs2857466	GAS2L1	cis	hippocampus	BrainEAC
rs2857466	SRRD	cis	parietal	SCAN
rs2857466	GAS2L1	cis	thalamus	BrainEAC
rs2857466	DUSP18	cis	parietal	SCAN
rs2857466	RASL10A	cis	cerebellum	SCAN
rs2857466	GAS2L1	cis	brain	BrainEAC
rs2857466	GAS2L1	cis	frontal cortex	BrainEAC
rs2857466	GAS2L1	cis	cerebellar cortex	BrainEAC
rs2857466	GAS2L1	cis	occipital cortex	BrainEAC
rs2857466	GAS2L1	cis	temporal cortex	BrainEAC
rs2857466	GAS2L1	cis	putamen	BrainEAC

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29629000-29659400	Weak transcription	Brain Anterior Caudate	brain
2	chr22:29641600-29659800	Weak transcription	Ovary	ovary
3	chr22:29641600-29661800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr22:29641800-29657800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr22:29642000-29659600	Weak transcription	Colon Smooth Muscle	Colon
6	chr22:29642200-29659800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr22:29642600-29662400	Strong transcription	Fetal Intestine Small	intestine
8	chr22:29643600-29660400	Weak transcription	Fetal Kidney	kidney
9	chr22:29644600-29659800	Weak transcription	Brain Substantia Nigra	brain
10	chr22:29647400-29662000	Strong transcription	Fetal Stomach	stomach
11	chr22:29649000-29662400	Weak transcription	Fetal Brain Male	brain
12	chr22:29650200-29662600	Weak transcription	Stomach Mucosa	stomach
13	chr22:29650600-29659800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr22:29650600-29660000	Weak transcription	Primary T cells from cord blood	blood
15	chr22:29650600-29660200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr22:29650800-29659800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr22:29651000-29659600	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr22:29651000-29660000	Weak transcription	HepG2	liver
19	chr22:29651800-29659600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr22:29652200-29659800	Weak transcription	HMEC	breast
21	chr22:29652400-29660200	Weak transcription	NHEK	skin
22	chr22:29653400-29657800	Strong transcription	Fetal Muscle Leg	muscle
23	chr22:29653400-29658800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr22:29653400-29659800	Weak transcription	NHLF	lung
25	chr22:29653600-29659600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr22:29653600-29662200	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr22:29654000-29657800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr22:29654000-29659600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr22:29654000-29659800	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr22:29654200-29662600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr22:29654400-29659800	Weak transcription	Aorta	Aorta
32	chr22:29654400-29660000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr22:29654600-29659800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr22:29654600-29662200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr22:29654600-29662400	Weak transcription	Primary hematopoietic stem cells	blood
36	chr22:29654600-29662400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr22:29654600-29662600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr22:29654800-29662400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr22:29655200-29658800	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr22:29655200-29661200	Weak transcription	GM12878-XiMat	blood
41	chr22:29655400-29658000	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr22:29655400-29659800	Weak transcription	Osteobl	bone
43	chr22:29655600-29658000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr22:29655600-29659600	Weak transcription	Pancreas	Pancrea
45	chr22:29655600-29662800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr22:29655800-29659600	Weak transcription	A549	lung
47	chr22:29656200-29659600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr22:29656400-29659600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr22:29656400-29659800	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr22:29656600-29658000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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