Variant report

Variant	rs822508
Chromosome Location	chr1:155850558-155850559
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10908481	0.87[MEX][hapmap]
rs11264422	0.88[CEU][hapmap];0.81[CHB][hapmap]
rs12024880	0.82[ASN][1000 genomes]
rs12027412	0.82[ASN][1000 genomes]
rs12563627	0.88[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1749405	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1749410	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2993207	0.88[CEU][hapmap];0.94[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.88[ASN][1000 genomes]
rs3820594	0.80[JPT][hapmap];0.83[MEX][hapmap]
rs4661151	0.88[CEU][hapmap];0.93[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.82[ASN][1000 genomes]
rs4661175	0.88[CEU][hapmap];0.81[CHB][hapmap];0.91[MEX][hapmap]
rs488079	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.82[ASN][1000 genomes]
rs490498	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[MEX][hapmap]
rs539602	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs625658	0.88[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.82[ASN][1000 genomes]
rs656247	0.84[ASN][1000 genomes]
rs656737	0.85[ASN][1000 genomes]
rs670523	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[MEX][hapmap]
rs708611	0.82[CEU][hapmap];0.87[MKK][hapmap];0.89[TSI][hapmap]
rs729022	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517204	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7538214	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7541060	0.81[CEU][hapmap]
rs821551	0.85[CEU][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap]
rs822490	0.85[CEU][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs822504	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs822505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs860295	0.85[CEU][hapmap];0.80[JPT][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs822508	SLC39A1	cis	cerebellum	SCAN
rs822508	YY1AP1	cis	cerebellum	SCAN
rs822508	ROBLD3	cis	parietal	SCAN
rs822508	PRUNE	cis	cerebellum	SCAN
rs822508	FAM189B	cis	cerebellum	SCAN
rs822508	RIT1	cis	cerebellum	SCAN
rs822508	BCAN	cis	cerebellum	SCAN
rs822508	SPRR3	cis	parietal	SCAN
rs822508	ADAM15	cis	multi-tissue	Pritchard

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155830000-155869000	Weak transcription	Gastric	stomach
2	chr1:155830400-155865800	Weak transcription	Esophagus	oesophagus
3	chr1:155830600-155866800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:155830800-155852000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr1:155831000-155851000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:155831000-155862600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr1:155831000-155862800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:155831000-155863000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr1:155831200-155862800	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr1:155831400-155859000	Weak transcription	HUVEC	blood vessel
11	chr1:155836400-155866400	Weak transcription	Primary B cells from cord blood	blood
12	chr1:155837600-155863000	Weak transcription	Colonic Mucosa	Colon
13	chr1:155841400-155863000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr1:155841600-155850600	Weak transcription	NHDF-Ad	bronchial
15	chr1:155841800-155850600	Weak transcription	Spleen	Spleen
16	chr1:155841800-155869200	Weak transcription	Right Ventricle	heart
17	chr1:155842600-155863400	Weak transcription	Right Atrium	heart
18	chr1:155842800-155852600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:155842800-155853400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:155844000-155852000	Strong transcription	Fetal Stomach	stomach
21	chr1:155844000-155853600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:155844000-155862200	Weak transcription	Lung	lung
23	chr1:155844200-155853600	Weak transcription	NH-A	brain
24	chr1:155844200-155854200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:155844200-155855400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:155844400-155874000	Weak transcription	Fetal Brain Male	brain
27	chr1:155845200-155853400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:155846800-155852200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr1:155846800-155854000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:155847000-155860200	Strong transcription	Fetal Brain Female	brain
31	chr1:155847200-155860200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr1:155847400-155860400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:155847600-155857000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:155847600-155866400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr1:155847800-155853400	Strong transcription	Brain Anterior Caudate	brain
36	chr1:155847800-155853400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr1:155848200-155852400	Strong transcription	Brain Substantia Nigra	brain
38	chr1:155848800-155850600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:155849000-155851200	Enhancers	Fetal Intestine Small	intestine
40	chr1:155849000-155858000	Strong transcription	Brain Germinal Matrix	brain
41	chr1:155849400-155851400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:155849400-155851400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr1:155849400-155853200	Strong transcription	Fetal Muscle Trunk	muscle
44	chr1:155849400-155863000	Weak transcription	Rectal Smooth Muscle	rectum
45	chr1:155849600-155851400	Strong transcription	Aorta	Aorta
46	chr1:155849600-155852600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:155849600-155853000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:155849600-155853400	Strong transcription	Brain Hippocampus Middle	brain
49	chr1:155849600-155854400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:155849600-155862800	Weak transcription	Primary hematopoietic stem cells	blood

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