Variant report

Variant	rs17776131
Chromosome Location	chr10:51028791-51028792
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:51028291..51030720-chr10:51030786..51035251,4	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10508917	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11592062	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11598461	0.82[EUR][1000 genomes]
rs11599492	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11812185	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11813858	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12774346	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719813	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719843	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17719866	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2377698	0.82[AMR][1000 genomes]
rs34419748	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34714687	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35547965	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3877001	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4012652	0.81[EUR][1000 genomes]
rs4495813	0.82[EUR][1000 genomes]
rs4592357	0.82[AMR][1000 genomes]
rs4838566	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4838568	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4838573	0.80[AMR][1000 genomes]
rs4838575	0.86[AMR][1000 genomes]
rs5013289	0.86[AMR][1000 genomes]
rs61846901	0.80[AMR][1000 genomes]
rs61846915	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61846922	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61846925	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs61846931	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7067802	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7093312	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7921218	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs17776131	AGAP6	cis	Muscle Skeletal	GTEx
rs17776131	AGAP6	cis	Whole Blood	GTEx
rs17776131	AGAP6	cis	Esophagus Muscularis	GTEx
rs17776131	AGAP6	cis	Nerve Tibial	GTEx
rs17776131	CTGLF3	cis	multi-tissue	Pritchard
rs17776131	AGAP6	cis	lung	GTEx
rs17776131	AGAP6	cis	Esophagus Mucosa	GTEx
rs17776131	AGAP6	cis	Adipose Subcutaneous	GTEx
rs17776131	AGAP6	cis	Artery Tibial	GTEx
rs17776131	AGAP6	cis	Thyroid	GTEx
rs17776131	AGAP6	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 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	chr10:51021800-51032800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr10:51021800-51033400	Weak transcription	Osteobl	bone
5	chr10:51021800-51039600	Weak transcription	Psoas Muscle	Psoas
6	chr10:51022000-51030200	Weak transcription	Fetal Kidney	kidney
7	chr10:51022200-51034800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr10:51022600-51035800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr10:51022800-51030000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr10:51023000-51029200	Strong transcription	Monocytes-CD14+_RO01746	blood
11	chr10:51023000-51030400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr10:51023000-51031000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr10:51023000-51031000	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr10:51023200-51029000	Strong transcription	HUES64 Cell Line	embryonic stem cell
15	chr10:51023600-51031000	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr10:51024000-51036600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr10:51024000-51052800	Weak transcription	NHLF	lung
18	chr10:51024200-51034200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr10:51024200-51053200	Weak transcription	Fetal Brain Male	brain
20	chr10:51024600-51030200	Weak transcription	Fetal Lung	lung
21	chr10:51024600-51030400	Strong transcription	HepG2	liver
22	chr10:51024600-51030800	Strong transcription	Primary T helper cells PMA-I stimulated	--
23	chr10:51024600-51054800	Weak transcription	Fetal Heart	heart
24	chr10:51024800-51030800	Strong transcription	Fetal Muscle Leg	muscle
25	chr10:51025200-51029200	Strong transcription	Fetal Stomach	stomach
26	chr10:51025200-51029400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr10:51025200-51031000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr10:51025400-51029200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
29	chr10:51025400-51029200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:51025400-51029200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr10:51025400-51029200	Strong transcription	Placenta	Placenta
32	chr10:51025400-51029200	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr10:51025400-51030600	Strong transcription	Dnd41	blood
34	chr10:51025400-51031000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr10:51025400-51031000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr10:51025400-51031000	Strong transcription	Aorta	Aorta
37	chr10:51025400-51031000	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr10:51025400-51031000	Strong transcription	Fetal Muscle Trunk	muscle
39	chr10:51025600-51029200	Strong transcription	Hela-S3	cervix
40	chr10:51025600-51030600	Strong transcription	Ovary	ovary
41	chr10:51025600-51031000	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr10:51025800-51029400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr10:51025800-51037000	Strong transcription	Primary T cells from cord blood	blood
44	chr10:51025800-51047800	Weak transcription	HMEC	breast
45	chr10:51026200-51039000	Weak transcription	Colon Smooth Muscle	Colon
46	chr10:51026200-51039600	Weak transcription	Brain Hippocampus Middle	brain
47	chr10:51026400-51047200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr10:51026600-51030000	Strong transcription	Fetal Intestine Small	intestine
49	chr10:51027000-51029800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr10:51027200-51029200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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