Variant report

Variant	rs10769929
Chromosome Location	chr11:8628056-8628057
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	chr11:8626986..8629942-chr11:8631713..8635066,3	K562	blood:

Extended variants
information (count: 98 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10160430	0.84[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs10160804	0.96[CEU][hapmap];0.83[YRI][hapmap];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10160805	0.84[ASN][1000 genomes]
rs10444244	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs10444316	0.95[JPT][hapmap]
rs10743076	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs10743078	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10743079	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10743080	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10743082	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10769908	0.85[CEU][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap]
rs10769910	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs10769915	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10769916	0.85[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10769919	0.84[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10769920	0.88[AMR][1000 genomes]
rs10769923	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10769924	0.94[ASN][1000 genomes]
rs10840042	0.85[CEU][hapmap]
rs10840047	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs10840051	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs10840056	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs10840060	0.85[CEU][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs10840062	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs10840063	0.81[CEU][hapmap];0.95[JPT][hapmap]
rs10840065	0.85[CEU][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs10840077	0.84[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10840080	0.86[ASN][1000 genomes]
rs10840081	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10840083	0.81[ASW][hapmap];0.81[CEU][hapmap];0.84[CHD][hapmap];0.80[MEX][hapmap];0.86[YRI][hapmap]
rs10840084	0.84[CEU][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10840087	0.94[ASN][1000 genomes]
rs10840089	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11041929	0.96[CEU][hapmap]
rs11041950	0.94[JPT][hapmap]
rs11041974	0.81[ASN][1000 genomes]
rs11041978	0.85[CEU][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs11041982	0.92[CEU][hapmap]
rs11041983	0.85[ASN][1000 genomes]
rs11041985	0.85[ASN][1000 genomes]
rs11041986	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11041990	0.81[ASW][hapmap];0.81[CEU][hapmap];0.83[YRI][hapmap]
rs11041994	0.81[CEU][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes]
rs11041995	0.80[CEU][hapmap];0.86[YRI][hapmap]
rs11041999	0.85[ASN][1000 genomes]
rs11042002	0.94[ASN][1000 genomes]
rs12806736	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap]
rs1374262	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs1446464	0.96[CEU][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs1900272	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1900273	0.82[CHD][hapmap];0.90[JPT][hapmap]
rs2028882	0.85[CEU][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs2289921	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs2289923	0.96[CEU][hapmap]
rs2871753	0.84[CEU][hapmap];0.95[JPT][hapmap]
rs4131072	0.96[CEU][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4244804	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.80[MEX][hapmap]
rs4244806	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4344491	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs4405311	0.82[AMR][1000 genomes]
rs4418812	0.88[ASN][1000 genomes]
rs4520598	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4758067	0.96[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs4929929	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4929941	0.96[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4929942	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.94[ASN][1000 genomes]
rs4929943	0.81[CEU][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap]
rs4929949	0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4929950	0.96[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7101471	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs7112153	0.85[CEU][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs7126013	0.96[CEU][hapmap]
rs7126934	0.95[CEU][hapmap]
rs7127684	0.85[CEU][hapmap];0.95[JPT][hapmap]
rs725502	0.85[CEU][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap]
rs726007	0.96[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs7929120	1.00[CEU][hapmap];0.83[AMR][1000 genomes]
rs7931604	0.96[CEU][hapmap]
rs7934396	0.94[ASN][1000 genomes]
rs7939731	0.85[CEU][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs7945659	0.90[CHD][hapmap];0.95[JPT][hapmap]
rs7947670	0.83[CEU][hapmap];0.89[JPT][hapmap]
rs9284150	0.96[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9284151	0.96[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9300088	0.84[AMR][1000 genomes]
rs9300089	0.87[CEU][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes]
rs9300090	0.81[CEU][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9300091	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs9300092	0.85[CEU][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs9300093	0.83[CEU][hapmap];1.00[JPT][hapmap]
rs9300094	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs935370	0.84[CEU][hapmap]
rs9705083	0.81[CEU][hapmap]
rs9705253	0.84[ASN][1000 genomes]
rs9736791	0.85[CEU][hapmap];0.83[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs9737312	0.81[CEU][hapmap]

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	esv2751035	chr11:8431654-8685451	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv896983	chr11:8526643-8682465	ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10769929	STK33	cis	lymphoblastoid	seeQTL
rs10769929	ARFIP2	cis	parietal	SCAN
rs10769929	ST5	cis	cerebellum	SCAN
rs10769929	RPL27A	cis	cerebellum	SCAN
rs10769929	RPL27A	cis	parietal	SCAN
rs10769929	STK33	cis	parietal	SCAN
rs10769929	STK33	cis	cerebellum	SCAN
rs10769929	SNORA45	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8623400-8634200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:8623600-8632000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr11:8625200-8628600	Enhancers	Muscle Satellite Cultured Cells	--
4	chr11:8625400-8628400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr11:8625400-8628400	Enhancers	HSMM	muscle
6	chr11:8625600-8628800	Enhancers	HSMMtube	muscle
7	chr11:8626000-8629800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:8626000-8637000	Weak transcription	Fetal Intestine Small	intestine
9	chr11:8626000-8637200	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr11:8626000-8661600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:8626000-8661800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr11:8626200-8629000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr11:8626200-8637200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr11:8626200-8653000	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:8626400-8630000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:8626400-8630000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr11:8626400-8634000	Weak transcription	Placenta	Placenta
18	chr11:8626400-8634200	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr11:8626400-8636000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr11:8626400-8636200	Weak transcription	Stomach Smooth Muscle	stomach
21	chr11:8626400-8636800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr11:8626400-8637200	Weak transcription	Pancreas	Pancrea
23	chr11:8626400-8637400	Weak transcription	Adipose Nuclei	Adipose
24	chr11:8626400-8638400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr11:8626400-8638400	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr11:8626400-8643400	Weak transcription	Fetal Lung	lung
27	chr11:8626600-8630000	Weak transcription	NH-A	brain
28	chr11:8626600-8637200	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:8626600-8639600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:8626600-8648800	Weak transcription	Stomach Mucosa	stomach
31	chr11:8626800-8629800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr11:8626800-8630000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:8626800-8630000	Weak transcription	NHDF-Ad	bronchial
34	chr11:8626800-8630000	Weak transcription	NHLF	lung
35	chr11:8626800-8630000	Weak transcription	Osteobl	bone
36	chr11:8626800-8637000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:8626800-8637200	Weak transcription	Esophagus	oesophagus
38	chr11:8626800-8659600	Weak transcription	Hela-S3	cervix
39	chr11:8627400-8630000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr11:8627600-8637200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:8627800-8630000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:8627800-8637000	Weak transcription	HMEC	breast
43	chr11:8627800-8637200	Weak transcription	NHEK	skin
44	chr11:8627800-8642400	Weak transcription	A549	lung
45	chr11:8628000-8629600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:8628000-8635400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr11:8628000-8637000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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