Variant report

Variant	rs10828266
Chromosome Location	chr10:22098701-22098702
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:22086256..22088772-chr10:22096451..22099042,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10508639	0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10740991	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs10740997	0.82[MEX][hapmap]
rs10764328	0.84[MEX][hapmap]
rs10764330	1.00[CEU][hapmap];0.82[GIH][hapmap];0.82[MEX][hapmap]
rs10828264	1.00[CHB][hapmap]
rs1086899	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs11012794	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1243180	0.80[CEU][hapmap]
rs1243194	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs1243195	1.00[CHB][hapmap]
rs12571634	0.95[CEU][hapmap];0.85[MEX][hapmap]
rs1269454	1.00[CHB][hapmap]
rs2026092	1.00[CHB][hapmap]
rs2066270	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap]
rs2066271	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap]
rs2487512	0.80[CEU][hapmap]
rs2666750	0.80[CEU][hapmap]
rs2666753	0.80[CEU][hapmap]
rs2666754	0.90[CEU][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs2666756	0.81[CEU][hapmap]
rs2666757	0.94[CEU][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs2666759	0.94[CEU][hapmap]
rs2666760	0.85[CEU][hapmap]
rs2666761	0.81[EUR][1000 genomes]
rs2666763	0.83[EUR][1000 genomes]
rs2666768	0.95[CEU][hapmap]
rs2666769	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs2666771	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap]
rs2666772	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[MEX][hapmap]
rs2666775	0.95[CEU][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap]
rs2666776	0.95[CEU][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs2666779	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[MEX][hapmap]
rs2666782	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs2793353	0.82[AMR][1000 genomes]
rs2807968	0.89[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs2807971	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap]
rs2807977	1.00[CHB][hapmap]
rs2807978	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs2807979	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[MEX][hapmap]
rs2807983	0.80[CEU][hapmap]
rs2807984	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap]
rs2807985	0.89[CEU][hapmap];0.90[MEX][hapmap]
rs2807986	0.89[CEU][hapmap]
rs2807987	0.95[CEU][hapmap];0.95[MEX][hapmap]
rs2807988	0.85[CEU][hapmap]
rs2859622	0.95[CEU][hapmap]
rs2998360	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[MEX][hapmap]
rs3951780	0.85[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.85[MEX][hapmap]
rs4024198	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4146689	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap]
rs4364959	0.85[CEU][hapmap];0.95[MEX][hapmap]
rs4748775	0.83[CEU][hapmap]
rs4748776	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[MEX][hapmap]
rs4748777	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs4748779	0.95[CEU][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap]
rs6482190	0.83[ASN][1000 genomes]
rs6650129	0.82[MEX][hapmap]
rs7082663	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.90[MEX][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7089656	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap]
rs7910002	0.80[CEU][hapmap]
rs792453	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[MEX][hapmap]
rs792455	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs792456	0.89[CEU][hapmap]
rs806774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][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	nsv1052464	chr10:21856531-22220087	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv1802317	chr10:21866085-22288132	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv894947	chr10:21869609-22117913	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv1793816	chr10:22088054-22285371	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10828266	PSTPIP2	trans	lymphoblastoid	seeQTL
rs10828266	MLLT10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:22048000-22109000	Weak transcription	Ovary	ovary
2	chr10:22048400-22099200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr10:22048800-22114000	Weak transcription	Duodenum Mucosa	Duodenum
4	chr10:22066000-22113000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:22074200-22105200	Weak transcription	Lung	lung
6	chr10:22074400-22099200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr10:22074800-22099000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr10:22074800-22100800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr10:22074800-22123200	Weak transcription	Left Ventricle	heart
10	chr10:22085600-22102800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr10:22086200-22099200	Weak transcription	HSMM	muscle
12	chr10:22086800-22102000	Weak transcription	Pancreas	Pancrea
13	chr10:22087000-22102000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr10:22087400-22102800	Weak transcription	Stomach Smooth Muscle	stomach
15	chr10:22087400-22103000	Weak transcription	Primary B cells from cord blood	blood
16	chr10:22087800-22102400	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr10:22087800-22110600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr10:22088000-22099200	Weak transcription	Fetal Brain Male	brain
19	chr10:22088400-22102600	Weak transcription	Liver	Liver
20	chr10:22089400-22099000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr10:22091400-22110000	Weak transcription	Right Ventricle	heart
22	chr10:22091600-22102400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr10:22092600-22100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr10:22093000-22100200	Weak transcription	GM12878-XiMat	blood
25	chr10:22094800-22103800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr10:22095000-22099200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr10:22095000-22104400	Weak transcription	Rectal Smooth Muscle	rectum
28	chr10:22095000-22114200	Weak transcription	Fetal Lung	lung
29	chr10:22096400-22099000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr10:22096400-22099400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr10:22096400-22100200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr10:22096400-22105600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr10:22096600-22099600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr10:22096600-22101400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr10:22096600-22101800	Weak transcription	Fetal Brain Female	brain
36	chr10:22096600-22102600	Weak transcription	Fetal Heart	heart
37	chr10:22096600-22104600	Weak transcription	Primary T cells from cord blood	blood
38	chr10:22096600-22105000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr10:22097000-22102800	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr10:22097600-22103000	Weak transcription	Brain Angular Gyrus	brain
41	chr10:22097800-22098800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
42	chr10:22097800-22099000	Weak transcription	K562	blood
43	chr10:22097800-22099600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:22097800-22099800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr10:22097800-22099800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr10:22097800-22099800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr10:22097800-22102200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr10:22097800-22102600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr10:22097800-22105200	Weak transcription	Esophagus	oesophagus
50	chr10:22098000-22099400	Weak transcription	HUES64 Cell Line	embryonic stem cell

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