Variant report

Variant	rs9888128
Chromosome Location	chr10:49620267-49620268
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:49615995..49618408-chr10:49619011..49621814,2	K562	blood:
2	chr10:49613649..49616466-chr10:49619116..49621899,2	K562	blood:
3	chr10:49620234..49623060-chr10:49677590..49681287,3	K562	blood:
4	chr10:49600536..49602318-chr10:49619238..49621122,2	K562	blood:
5	chr10:49619514..49622153-chr10:49622504..49625064,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10218874	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10437448	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10508901	0.81[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10508903	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1051507	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1051508	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1051509	0.92[CEU][hapmap];0.90[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10745266	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10745269	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10745270	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10776595	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10776596	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10776598	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10776600	0.82[EUR][1000 genomes]
rs10857560	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10857561	0.87[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10857562	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10857566	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11101290	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11101298	0.83[EUR][1000 genomes]
rs11101306	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11101317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11101318	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11101320	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11598434	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12411830	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs1345103	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1919708	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1919712	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs1919713	0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2017750	0.90[CHB][hapmap];0.95[CHD][hapmap];0.81[ASN][1000 genomes]
rs2263102	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2289805	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2377351	0.82[CEU][hapmap];0.94[CHB][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2440861	0.85[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2463959	0.85[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2463960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2590381	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2698761	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[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2698766	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2698767	0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2889611	0.81[CHB][hapmap];0.82[CHD][hapmap]
rs2921271	0.83[ASN][1000 genomes]
rs3789320	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3827680	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][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]
rs3827681	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs4838590	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6537560	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6537561	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7072515	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7075976	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7086070	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7086275	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7101060	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs734371	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7904142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7924070	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8428	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];0.92[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs867631	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs883604	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9284	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]

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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1039508	chr10:49595718-49654403	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9888128	ARHGAP22	cis	parietal	SCAN
rs9888128	SGMS1	cis	parietal	SCAN
rs9888128	MAPK8	cis	cerebellum	SCAN
rs9888128	MAPK8	cis	Thyroid	GTEx
rs9888128	MAPK8	cis	parietal	SCAN
rs9888128	MAPK8	cis	normal skin	skin_eQTL
rs9888128	MSMB	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49599200-49622200	Weak transcription	HepG2	liver
2	chr10:49607600-49624200	Weak transcription	Gastric	stomach
3	chr10:49607600-49624200	Weak transcription	Lung	lung
4	chr10:49607600-49647800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:49607600-49652400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr10:49607800-49620400	Weak transcription	Stomach Mucosa	stomach
7	chr10:49608000-49645600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr10:49608200-49621000	Weak transcription	Small Intestine	intestine
9	chr10:49608200-49634400	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr10:49609000-49620600	Weak transcription	Hela-S3	cervix
11	chr10:49609200-49620800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr10:49609800-49620600	Weak transcription	Brain Substantia Nigra	brain
13	chr10:49611200-49620600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr10:49612000-49664200	Weak transcription	Thymus	Thymus
15	chr10:49612800-49660200	Weak transcription	Aorta	Aorta
16	chr10:49614600-49622200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr10:49614600-49623000	Weak transcription	Pancreas	Pancrea
18	chr10:49614800-49620600	Weak transcription	Fetal Heart	heart
19	chr10:49614800-49638400	Weak transcription	HUVEC	blood vessel
20	chr10:49615000-49621200	Weak transcription	NHLF	lung
21	chr10:49615000-49622000	Weak transcription	NHEK	skin
22	chr10:49615000-49622600	Weak transcription	HMEC	breast
23	chr10:49615400-49620600	Weak transcription	HSMMtube	muscle
24	chr10:49615600-49620600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr10:49616000-49621600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr10:49616000-49621800	Strong transcription	Dnd41	blood
27	chr10:49616200-49621400	Strong transcription	Placenta	Placenta
28	chr10:49616400-49620800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr10:49616600-49621600	Strong transcription	Fetal Thymus	thymus
30	chr10:49616800-49621600	Strong transcription	Skeletal Muscle Female	skeletal muscle
31	chr10:49616800-49621800	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr10:49617200-49620600	Weak transcription	Ovary	ovary
33	chr10:49617200-49624200	Weak transcription	Left Ventricle	heart
34	chr10:49617400-49621400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
35	chr10:49617800-49621200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr10:49618000-49620400	Strong transcription	A549	lung
37	chr10:49618000-49620600	Strong transcription	Brain Cingulate Gyrus	brain
38	chr10:49618000-49621200	Strong transcription	HSMM	muscle
39	chr10:49618000-49621400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr10:49618200-49620600	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr10:49618200-49621400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr10:49618200-49621400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr10:49618200-49621600	Strong transcription	Fetal Kidney	kidney
44	chr10:49618400-49620800	ZNF genes & repeats	K562	blood
45	chr10:49618400-49621200	ZNF genes & repeats	Primary T cells from cord blood	blood
46	chr10:49618400-49621400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr10:49618400-49621600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr10:49618400-49621600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr10:49618600-49621000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
50	chr10:49618800-49620400	Weak transcription	NHDF-Ad	bronchial

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