Variant report

Variant	rs1438928
Chromosome Location	chr10:51043786-51043787
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	chr10:51033722..51037906-chr10:51041660..51043995,3	K562	blood:
2	chr10:51038398..51040460-chr10:51042005..51043947,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10857546	0.81[AMR][1000 genomes]
rs11101238	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1258193	0.80[EUR][1000 genomes]
rs1258194	0.81[EUR][1000 genomes]
rs1258232	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1438929	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720394	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3793805	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3849145	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4390270	0.81[AFR][1000 genomes]
rs7075365	0.82[AFR][1000 genomes]
rs8474	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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	esv2758219	chr10:50971974-51925166	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	esv2759749	chr10:50971974-51925166	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv428232	chr10:50971974-51925166	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv895379	chr10:51022933-51187793	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1438928	AGAP6	cis	Thyroid	GTEx
rs1438928	AGAP6	cis	Esophagus Mucosa	GTEx
rs1438928	AGAP6	cis	Artery Tibial	GTEx
rs1438928	AGAP6	cis	Nerve Tibial	GTEx
rs1438928	AGAP6	cis	Esophagus Muscularis	GTEx
rs1438928	AGAP6	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:51019800-51053400	Weak transcription	Small Intestine	intestine
2	chr10:51020400-51049600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr10:51024000-51052800	Weak transcription	NHLF	lung
4	chr10:51024200-51053200	Weak transcription	Fetal Brain Male	brain
5	chr10:51024600-51054800	Weak transcription	Fetal Heart	heart
6	chr10:51025800-51047800	Weak transcription	HMEC	breast
7	chr10:51026400-51047200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr10:51028200-51046600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr10:51028200-51047000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr10:51028200-51050000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr10:51028200-51053000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr10:51028200-51054600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr10:51028400-51049600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr10:51028400-51053000	Weak transcription	Colonic Mucosa	Colon
15	chr10:51028400-51055000	Weak transcription	Spleen	Spleen
16	chr10:51028400-51056200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr10:51028600-51051400	Weak transcription	Fetal Brain Female	brain
18	chr10:51030800-51043800	Weak transcription	Fetal Muscle Leg	muscle
19	chr10:51031000-51046800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr10:51031000-51053200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr10:51033200-51052000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr10:51033400-51045800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr10:51035800-51043800	Weak transcription	HSMM	muscle
24	chr10:51037000-51043800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr10:51038200-51052000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr10:51038800-51052000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr10:51039800-51043800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr10:51039800-51043800	Weak transcription	Fetal Kidney	kidney
29	chr10:51039800-51052800	Weak transcription	NHDF-Ad	bronchial
30	chr10:51040000-51051200	Weak transcription	HSMMtube	muscle
31	chr10:51040000-51051800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr10:51040000-51053400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr10:51040200-51047600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr10:51040400-51046600	Weak transcription	NH-A	brain
35	chr10:51040400-51047000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr10:51040400-51047000	Weak transcription	Lung	lung
37	chr10:51040400-51047200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr10:51040400-51049800	Weak transcription	Brain Germinal Matrix	brain
39	chr10:51040400-51049800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr10:51040400-51050600	Weak transcription	Psoas Muscle	Psoas
41	chr10:51040400-51053200	Weak transcription	Brain Hippocampus Middle	brain
42	chr10:51040400-51053200	Weak transcription	Esophagus	oesophagus
43	chr10:51040600-51043800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr10:51040600-51045600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr10:51040600-51047200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr10:51040600-51048200	Weak transcription	Fetal Lung	lung
47	chr10:51040600-51049800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr10:51040600-51049800	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr10:51040600-51051600	Weak transcription	Right Ventricle	heart
50	chr10:51040600-51052000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links