Variant report

Variant	rs1438929
Chromosome Location	chr10:51043865-51043866
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr10:51043800-51044341	SH-SY5Y	brain:	n/a	n/a
2	CTCF	chr10:51043800-51043950	Caco-2	colon:	n/a	n/a
3	CEBPB	chr10:51043833-51044157	HepG2	liver:	n/a	n/a
4	CEBPB	chr10:51043820-51044146	H1-hESC	embryonic stem cell:	n/a	n/a

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:

Variant related genes	Relation type
PARG	TF binding region

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]
rs1438928	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
rs1438929	AGAP6	cis	Artery Tibial	GTEx
rs1438929	AGAP6	cis	Nerve Tibial	GTEx
rs1438929	AGAP6	cis	Esophagus Muscularis	GTEx
rs1438929	AGAP6	cis	Adipose Subcutaneous	GTEx
rs1438929	AGAP6	cis	Thyroid	GTEx
rs1438929	AGAP6	cis	Esophagus Mucosa	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	chr10:51031000-51046800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr10:51031000-51053200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr10:51033200-51052000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:51033400-51045800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr10:51038200-51052000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr10:51038800-51052000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr10:51039800-51052800	Weak transcription	NHDF-Ad	bronchial
25	chr10:51040000-51051200	Weak transcription	HSMMtube	muscle
26	chr10:51040000-51051800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr10:51040000-51053400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr10:51040200-51047600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr10:51040400-51046600	Weak transcription	NH-A	brain
30	chr10:51040400-51047000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr10:51040400-51047000	Weak transcription	Lung	lung
32	chr10:51040400-51047200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr10:51040400-51049800	Weak transcription	Brain Germinal Matrix	brain
34	chr10:51040400-51049800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr10:51040400-51050600	Weak transcription	Psoas Muscle	Psoas
36	chr10:51040400-51053200	Weak transcription	Brain Hippocampus Middle	brain
37	chr10:51040400-51053200	Weak transcription	Esophagus	oesophagus
38	chr10:51040600-51045600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr10:51040600-51047200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr10:51040600-51048200	Weak transcription	Fetal Lung	lung
41	chr10:51040600-51049800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr10:51040600-51049800	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr10:51040600-51051600	Weak transcription	Right Ventricle	heart
44	chr10:51040600-51052000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr10:51040600-51053000	Weak transcription	Brain Substantia Nigra	brain
46	chr10:51040600-51053000	Weak transcription	Gastric	stomach
47	chr10:51040600-51053200	Weak transcription	Brain Angular Gyrus	brain
48	chr10:51040600-51053200	Weak transcription	Brain Cingulate Gyrus	brain
49	chr10:51040600-51053400	Weak transcription	Brain Anterior Caudate	brain
50	chr10:51040600-51053400	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links