Variant report

Variant	rs10460358
Chromosome Location	chr2:172295794-172295795
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172288399..172297381-chr2:172370978..172381493,22	K562	blood:
2	chr2:172294486..172297106-chr2:172372290..172374923,2	K562	blood:
3	chr2:172012919..172015830-chr2:172294656..172296953,2	K562	blood:
4	chr2:172287467..172293160-chr2:172293206..172300397,21	K562	blood:
5	chr2:172016674..172018402-chr2:172295165..172296770,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000071967	Chromatin interaction
ENSG00000233762	Chromatin interaction
ENSG00000198586	Chromatin interaction
ENSG00000115827	Chromatin interaction
ENSG00000123600	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10930473	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11677562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11679641	0.84[ASW][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.92[MEX][hapmap];0.80[MKK][hapmap];0.80[ASN][1000 genomes]
rs12052810	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12465868	0.88[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs12469151	0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs12471094	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12616940	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1558963	0.95[JPT][hapmap];0.92[MEX][hapmap]
rs17285260	0.84[ASW][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap]
rs1921776	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2058927	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2356709	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs55862836	0.81[ASN][1000 genomes]
rs62181358	0.84[AMR][1000 genomes]
rs62183460	0.82[ASN][1000 genomes]
rs6747400	0.95[JPT][hapmap];0.92[MEX][hapmap]
rs727231	0.92[MEX][hapmap]
rs7590275	1.00[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs997666	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	esv3349868	chr2:172276494-172302401	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
3	esv1832950	chr2:172283513-172488111	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10460358	GAD1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172291000-172319800	Weak transcription	Stomach Mucosa	stomach
2	chr2:172291400-172296200	Weak transcription	Lung	lung
3	chr2:172291400-172296200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:172291400-172296200	Weak transcription	Spleen	Spleen
5	chr2:172291400-172296400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:172291400-172296400	Weak transcription	Aorta	Aorta
7	chr2:172291400-172296400	Weak transcription	Small Intestine	intestine
8	chr2:172291400-172297800	Weak transcription	Esophagus	oesophagus
9	chr2:172291400-172297800	Weak transcription	Gastric	stomach
10	chr2:172291600-172296000	Weak transcription	Right Ventricle	heart
11	chr2:172291600-172297800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:172291600-172304000	Weak transcription	Pancreas	Pancrea
13	chr2:172291600-172305200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:172291600-172311800	Weak transcription	Fetal Brain Male	brain
15	chr2:172291800-172296400	Weak transcription	Brain Germinal Matrix	brain
16	chr2:172291800-172296400	Weak transcription	Colonic Mucosa	Colon
17	chr2:172291800-172296600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:172291800-172297800	Weak transcription	HSMMtube	muscle
19	chr2:172291800-172300000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr2:172291800-172306400	Weak transcription	Psoas Muscle	Psoas
21	chr2:172291800-172338200	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr2:172292000-172296000	Weak transcription	Thymus	Thymus
23	chr2:172292000-172296400	Weak transcription	Stomach Smooth Muscle	stomach
24	chr2:172292000-172297200	Weak transcription	NHLF	lung
25	chr2:172292000-172304400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr2:172292000-172312800	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:172292000-172341600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:172292200-172297400	Weak transcription	Hela-S3	cervix
29	chr2:172292400-172296000	Weak transcription	Fetal Brain Female	brain
30	chr2:172292400-172296200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr2:172292400-172298600	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr2:172292400-172299400	Strong transcription	Fetal Muscle Leg	muscle
33	chr2:172292400-172301200	Strong transcription	Placenta	Placenta
34	chr2:172292400-172301800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr2:172292600-172295800	Strong transcription	Brain Cingulate Gyrus	brain
36	chr2:172292600-172297000	Weak transcription	Brain Substantia Nigra	brain
37	chr2:172292600-172297200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr2:172292600-172297400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr2:172292600-172298000	Strong transcription	Primary B cells from cord blood	blood
40	chr2:172292600-172298600	Strong transcription	Primary hematopoietic stem cells	blood
41	chr2:172292600-172301200	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr2:172292600-172301400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr2:172292600-172302000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:172292600-172302600	Strong transcription	Liver	Liver
45	chr2:172292600-172302800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:172292600-172307200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:172292600-172311600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:172292600-172312000	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr2:172292600-172317600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr2:172292600-172320400	Strong transcription	Primary T helper cells fromperipheralblood	blood

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