Variant report

Variant	rs11042023
Chromosome Location	chr11:8662516-8662517
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10128597	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10769908	0.84[MEX][hapmap]
rs10769931	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10769932	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10769936	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs10769938	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10769939	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840099	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840100	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840102	0.98[ASN][1000 genomes]
rs10840104	0.98[ASN][1000 genomes]
rs11041978	0.84[MEX][hapmap]
rs11042016	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11042017	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042018	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11042025	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11042029	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11042030	0.98[ASN][1000 genomes]
rs12271470	0.97[ASN][1000 genomes]
rs12575252	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12803166	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1502317	0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2028882	0.84[MEX][hapmap]
rs2316901	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34867877	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35319120	1.00[ASN][1000 genomes]
rs36092927	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4256980	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4272783	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4291677	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4495896	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4503528	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4929923	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4929924	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4929925	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4929926	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4929927	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4929928	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4929942	0.84[MEX][hapmap]
rs4929943	0.84[MEX][hapmap]
rs4929947	0.89[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4929948	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6486253	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7110529	0.92[ASN][1000 genomes]
rs7113874	0.94[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7118611	0.98[ASN][1000 genomes]
rs7126235	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs725502	0.84[MEX][hapmap]
rs7939673	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7939731	0.84[MEX][hapmap]
rs7941510	0.98[ASN][1000 genomes]
rs7945659	0.91[MEX][hapmap]
rs7950166	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7950528	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs885114	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9300092	0.84[MEX][hapmap]
rs9736791	0.84[MEX][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

Variant related diseases (count:1)

Disease	PMID	Source
Obesity	23563607	GWAS catalog

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11042023	SNORA45	cis	parietal	SCAN
rs11042023	OR52E2	cis	parietal	SCAN
rs11042023	RPL27A	cis	cerebellum	SCAN
rs11042023	OR56B4	cis	parietal	SCAN
rs11042023	SNORA45	cis	cerebellum	SCAN
rs11042023	IPO7	cis	cerebellum	SCAN
rs11042023	CNGA4	cis	cerebellum	SCAN
rs11042023	OR51V1	cis	cerebellum	SCAN
rs11042023	TRIM66	cis	Whole Blood	GTEx
rs11042023	OR10A4	cis	parietal	SCAN
rs11042023	RPL27A	cis	parietal	SCAN
rs11042023	PKD1L2	trans	cerebellum	SCAN
rs11042023	STK33	cis	cerebellum	SCAN
rs11042023	SWAP70	cis	cerebellum	SCAN
rs11042023	ST5	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:8632800-8663800	Weak transcription	Fetal Kidney	kidney
2	chr11:8637000-8703200	Weak transcription	Small Intestine	intestine
3	chr11:8641800-8666200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr11:8644800-8663400	Weak transcription	Fetal Lung	lung
5	chr11:8644800-8667000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:8646200-8671000	Weak transcription	HUVEC	blood vessel
7	chr11:8646400-8666400	Weak transcription	HSMM	muscle
8	chr11:8649600-8665400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr11:8650800-8676200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr11:8652200-8675000	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr11:8653400-8663800	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr11:8653400-8664000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr11:8653400-8667000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr11:8654000-8673800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr11:8654200-8663200	Weak transcription	Fetal Brain Male	brain
16	chr11:8654200-8673800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr11:8654200-8675600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr11:8654400-8672400	Strong transcription	Brain Anterior Caudate	brain
19	chr11:8655000-8662600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr11:8655000-8664200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr11:8655000-8664200	Strong transcription	Fetal Stomach	stomach
22	chr11:8655000-8670200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:8655000-8676400	Strong transcription	Primary T cells from cord blood	blood
24	chr11:8655200-8664200	Strong transcription	Brain Hippocampus Middle	brain
25	chr11:8655200-8664400	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr11:8655200-8664800	Strong transcription	Lung	lung
27	chr11:8655200-8665000	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr11:8655200-8672600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:8655400-8666600	Weak transcription	Fetal Thymus	thymus
30	chr11:8655400-8673400	Strong transcription	Dnd41	blood
31	chr11:8655600-8664400	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr11:8655600-8670600	Strong transcription	Adipose Nuclei	Adipose
33	chr11:8656000-8670600	Strong transcription	Fetal Muscle Leg	muscle
34	chr11:8656000-8672600	Strong transcription	Skeletal Muscle Female	skeletal muscle
35	chr11:8656000-8672800	Strong transcription	Placenta	Placenta
36	chr11:8656400-8662600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr11:8656400-8662800	Strong transcription	Ovary	ovary
38	chr11:8656600-8671600	Strong transcription	Brain Cingulate Gyrus	brain
39	chr11:8656800-8666800	Weak transcription	HMEC	breast
40	chr11:8657000-8663400	Strong transcription	Pancreas	Pancrea
41	chr11:8657200-8663600	Weak transcription	Fetal Brain Female	brain
42	chr11:8657200-8673800	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr11:8657400-8662600	Strong transcription	Thymus	Thymus
44	chr11:8657400-8672600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:8658000-8666400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr11:8658000-8675200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr11:8658200-8672400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr11:8658200-8673800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr11:8658400-8664200	Strong transcription	Primary B cells from cord blood	blood
50	chr11:8658400-8664200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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