Variant report

Variant	rs17124739
Chromosome Location	chr11:120924671-120924672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10502245	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10892662	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10892663	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10892664	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10892665	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10892666	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10892667	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs10892668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10892669	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10892670	0.95[ASN][1000 genomes]
rs11218115	0.90[ASN][1000 genomes]
rs11218118	0.93[ASN][1000 genomes]
rs11218120	0.93[ASN][1000 genomes]
rs11218121	0.93[ASN][1000 genomes]
rs11218122	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11218123	0.94[ASN][1000 genomes]
rs11218125	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11218126	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11218127	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11218128	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs11218135	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11218137	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11218139	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11218140	0.92[ASN][1000 genomes]
rs12225989	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12226639	0.96[ASN][1000 genomes]
rs12274032	0.98[ASN][1000 genomes]
rs12274094	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12283211	0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs12576572	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs12576574	0.93[ASN][1000 genomes]
rs12576758	0.93[ASN][1000 genomes]
rs12576759	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12577611	0.93[ASN][1000 genomes]
rs17124764	0.96[ASN][1000 genomes]
rs1939004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2000525	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2000526	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2000527	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2000528	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2186601	0.96[ASN][1000 genomes]
rs2298491	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs34929374	0.83[ASN][1000 genomes]
rs3758891	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3824976	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4396299	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4594010	0.94[ASN][1000 genomes]
rs56675723	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57401958	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57826163	0.98[ASN][1000 genomes]
rs58204590	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61903185	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6589854	0.96[ASN][1000 genomes]
rs6589855	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6589856	0.96[ASN][1000 genomes]
rs67932968	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs68097814	0.93[ASN][1000 genomes]
rs7122879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7478744	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7927356	0.96[ASN][1000 genomes]
rs7928550	0.88[ASN][1000 genomes]
rs7931603	0.96[ASN][1000 genomes]
rs7940619	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7947565	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7952619	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][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	nsv1046688	chr11:120894391-120956305	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	nsv1039908	chr11:120904893-120936907	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17124739	TBCEL	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120896000-120938600	Weak transcription	Lung	lung
2	chr11:120896200-120959600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr11:120896600-120938200	Weak transcription	Fetal Stomach	stomach
4	chr11:120898800-120938400	Weak transcription	Aorta	Aorta
5	chr11:120900800-120949800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr11:120905800-120941600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr11:120909000-120956400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:120910000-120966600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr11:120910200-120938200	Weak transcription	Small Intestine	intestine
10	chr11:120910200-120939600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:120911200-120939600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:120911200-120957400	Weak transcription	Thymus	Thymus
13	chr11:120911200-120961200	Weak transcription	Spleen	Spleen
14	chr11:120914000-120948400	Weak transcription	Fetal Heart	heart
15	chr11:120915400-120929400	Strong transcription	Primary hematopoietic stem cells	blood
16	chr11:120915400-120950200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr11:120915600-120931600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:120915600-120941200	Strong transcription	Primary T cells from cord blood	blood
19	chr11:120915800-120935400	Strong transcription	Fetal Lung	lung
20	chr11:120915800-120940000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr11:120916200-120925000	Weak transcription	NHDF-Ad	bronchial
22	chr11:120916200-120939400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:120916400-120929200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr11:120916400-120940600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:120916600-120927400	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr11:120916600-120935000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr11:120916600-120940200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:120916800-120941000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr11:120916800-120942400	Weak transcription	Esophagus	oesophagus
30	chr11:120917200-120927000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr11:120918000-120938200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr11:120918400-120925000	Weak transcription	Brain Germinal Matrix	brain
33	chr11:120918400-120942600	Weak transcription	Gastric	stomach
34	chr11:120919000-120927200	Weak transcription	HMEC	breast
35	chr11:120919800-120934800	Weak transcription	A549	lung
36	chr11:120919800-120936000	Weak transcription	Fetal Intestine Small	intestine
37	chr11:120920000-120942000	Weak transcription	Stomach Mucosa	stomach
38	chr11:120920400-120942400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:120921400-120930200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr11:120922000-120929400	Strong transcription	Primary B cells from cord blood	blood
41	chr11:120922000-120929800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr11:120922200-120927400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr11:120922200-120927400	Strong transcription	Fetal Kidney	kidney
44	chr11:120922200-120927800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr11:120922200-120928600	Strong transcription	Liver	Liver
46	chr11:120922200-120931400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:120922200-120937000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr11:120922200-120937000	Strong transcription	HSMM	muscle
49	chr11:120922200-120937400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr11:120922200-120940600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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