Variant report

Variant	rs11101238
Chromosome Location	chr10:51029279-51029280
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	chr10:51028291..51030720-chr10:51030786..51035251,4	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10857546	0.83[AMR][1000 genomes]
rs1258193	0.81[EUR][1000 genomes]
rs1258194	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1258232	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1438928	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1438929	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1720394	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3793805	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3849145	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8474	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11101238	AGAP6	cis	Thyroid	GTEx
rs11101238	AGAP6	cis	Artery Tibial	GTEx
rs11101238	AGAP6	cis	Nerve Tibial	GTEx
rs11101238	AGAP6	cis	Adipose Subcutaneous	GTEx
rs11101238	PARG,AGAP4,AGAP9,AGAP5,AGAP8,AGAP10,AGAP6,AGAP7,LOC727726,LOC728407,LOC100133130,LOC399753,LOC100294038	cis	cerebellar cortex	BrainEAC
rs11101238	AGAP6	cis	Esophagus Muscularis	GTEx
rs11101238	AGAP6	cis	Esophagus Mucosa	GTEx
rs11101238	PARG,AGAP4,AGAP9,AGAP5,AGAP8,AGAP10,AGAP6,AGAP7,LOC727726,LOC728407,LOC100133130,LOC399753,LOC100294038	cis	brain	BrainEAC

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	chr10:51023000-51030400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr10:51023000-51031000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr10:51023000-51031000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr10:51023600-51031000	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr10:51024000-51036600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr10:51024000-51052800	Weak transcription	NHLF	lung
16	chr10:51024200-51034200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr10:51024200-51053200	Weak transcription	Fetal Brain Male	brain
18	chr10:51024600-51030200	Weak transcription	Fetal Lung	lung
19	chr10:51024600-51030400	Strong transcription	HepG2	liver
20	chr10:51024600-51030800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr10:51024600-51054800	Weak transcription	Fetal Heart	heart
22	chr10:51024800-51030800	Strong transcription	Fetal Muscle Leg	muscle
23	chr10:51025200-51029400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr10:51025200-51031000	Strong transcription	Duodenum Mucosa	Duodenum
25	chr10:51025400-51030600	Strong transcription	Dnd41	blood
26	chr10:51025400-51031000	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr10:51025400-51031000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr10:51025400-51031000	Strong transcription	Aorta	Aorta
29	chr10:51025400-51031000	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr10:51025400-51031000	Strong transcription	Fetal Muscle Trunk	muscle
31	chr10:51025600-51030600	Strong transcription	Ovary	ovary
32	chr10:51025600-51031000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr10:51025800-51029400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr10:51025800-51037000	Strong transcription	Primary T cells from cord blood	blood
35	chr10:51025800-51047800	Weak transcription	HMEC	breast
36	chr10:51026200-51039000	Weak transcription	Colon Smooth Muscle	Colon
37	chr10:51026200-51039600	Weak transcription	Brain Hippocampus Middle	brain
38	chr10:51026400-51047200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr10:51026600-51030000	Strong transcription	Fetal Intestine Small	intestine
40	chr10:51027000-51029800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr10:51027200-51038000	Weak transcription	HUVEC	blood vessel
42	chr10:51027400-51030600	Weak transcription	NHDF-Ad	bronchial
43	chr10:51027600-51034400	Weak transcription	HSMMtube	muscle
44	chr10:51027600-51034800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr10:51027800-51030200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr10:51027800-51039400	Weak transcription	Esophagus	oesophagus
47	chr10:51028000-51030000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr10:51028000-51030000	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr10:51028000-51039400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr10:51028000-51039600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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