Variant report

Variant	rs11592809
Chromosome Location	chr10:97366817-97366818
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	chr10:97129620..97132009-chr10:97364748..97367399,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11592789	0.89[CEU][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs11593038	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11593693	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11594687	0.81[EUR][1000 genomes]
rs11595122	0.89[CEU][hapmap]
rs11595248	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11598540	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12354465	1.00[CHB][hapmap]
rs12357513	1.00[CHB][hapmap]
rs12359410	1.00[CHB][hapmap]
rs12761112	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12761960	0.89[CEU][hapmap]
rs12763743	0.81[EUR][1000 genomes]
rs12765494	0.88[EUR][1000 genomes]
rs12767650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12770313	0.89[CEU][hapmap]
rs12770849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12774334	0.84[AMR][1000 genomes]
rs12775780	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12779833	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12780375	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12781327	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12782273	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1409710	0.89[CEU][hapmap];1.00[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]
rs2275272	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2296690	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3176886	0.84[EUR][1000 genomes]
rs3176888	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34296389	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34332904	0.87[EUR][1000 genomes]
rs34460407	0.81[EUR][1000 genomes]
rs34533159	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34832675	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34847853	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35700869	0.89[CEU][hapmap];0.95[TSI][hapmap]
rs35712039	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3765571	0.90[CHD][hapmap];1.00[ASN][1000 genomes]
rs3793746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs3793751	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493193	1.00[LWK][hapmap]
rs533383	1.00[LWK][hapmap]
rs568046	1.00[LWK][hapmap]
rs57670810	0.89[EUR][1000 genomes]
rs67857430	0.81[EUR][1000 genomes]
rs7073937	1.00[CHB][hapmap]
rs71482367	0.85[EUR][1000 genomes]
rs71482376	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71482377	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs71482378	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526180	chr10:97332195-97511037	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv531923	chr10:97366055-97725757	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11592809	PIPSL	cis	parietal	SCAN
rs11592809	CPEB3	cis	cerebellum	SCAN
rs11592809	C10orf12	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97335200-97373400	Weak transcription	Psoas Muscle	Psoas
2	chr10:97361000-97367600	Weak transcription	Fetal Kidney	kidney
3	chr10:97361000-97368200	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr10:97361000-97368400	Weak transcription	Brain Hippocampus Middle	brain
5	chr10:97361600-97367800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr10:97361800-97369200	Weak transcription	Primary B cells from cord blood	blood
7	chr10:97363200-97369000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr10:97363400-97370400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr10:97363400-97370400	Strong transcription	Fetal Intestine Small	intestine
10	chr10:97363600-97369200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr10:97363800-97367600	Enhancers	Colon Smooth Muscle	Colon
12	chr10:97363800-97368400	Weak transcription	Brain Substantia Nigra	brain
13	chr10:97363800-97369200	Weak transcription	HMEC	breast
14	chr10:97363800-97369800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr10:97364000-97367400	Enhancers	Rectal Smooth Muscle	rectum
16	chr10:97364000-97370200	Strong transcription	Small Intestine	intestine
17	chr10:97364000-97382000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr10:97364000-97409200	Strong transcription	Primary T cells from cord blood	blood
19	chr10:97364000-97411000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr10:97364200-97367000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr10:97364200-97372000	Strong transcription	Fetal Intestine Large	intestine
22	chr10:97364400-97367200	Genic enhancers	Fetal Stomach	stomach
23	chr10:97364400-97370000	Weak transcription	Fetal Brain Male	brain
24	chr10:97364400-97373200	Strong transcription	Liver	Liver
25	chr10:97364400-97378600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr10:97364400-97378600	Strong transcription	Fetal Brain Female	brain
27	chr10:97364400-97378600	Strong transcription	Spleen	Spleen
28	chr10:97364400-97379000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr10:97364400-97403200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr10:97364600-97369000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr10:97364600-97372800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr10:97364600-97377400	Strong transcription	Placenta	Placenta
33	chr10:97364600-97378600	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr10:97364600-97378600	Strong transcription	Pancreas	Pancrea
35	chr10:97364600-97378800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr10:97364600-97378800	Strong transcription	NH-A	brain
37	chr10:97364600-97379000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr10:97364600-97379000	Strong transcription	GM12878-XiMat	blood
39	chr10:97364600-97388400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr10:97364800-97368000	Strong transcription	Thymus	Thymus
41	chr10:97364800-97368200	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr10:97364800-97368600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr10:97364800-97369000	Weak transcription	Right Ventricle	heart
44	chr10:97364800-97372200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr10:97364800-97372600	Strong transcription	HepG2	liver
46	chr10:97364800-97378600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr10:97364800-97378600	Strong transcription	Gastric	stomach
48	chr10:97364800-97378800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr10:97364800-97378800	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr10:97364800-97378800	Strong transcription	Osteobl	bone

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