Variant report

Variant	rs557483
Chromosome Location	chr11:74614605-74614606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs11236269	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11605604	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12363224	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1282460	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1282461	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1282689	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1282690	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1282692	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1282695	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1292895	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1297319	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1315297	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1583342	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2028343	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2028344	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2033532	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs41531051	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs471462	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs473080	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs473256	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480840	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs483615	0.84[AMR][1000 genomes]
rs495246	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs502225	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs505688	0.84[AMR][1000 genomes]
rs508319	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs511021	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs511890	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs512780	0.85[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs513137	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs519741	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs527529	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs529249	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs529488	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs537054	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs538502	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs543244	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs546643	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs550491	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550869	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550980	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs561589	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs562265	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs565767	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs567956	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs568558	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568758	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs571446	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs573925	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577063	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs577102	0.82[AMR][1000 genomes]
rs580142	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs590105	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599722	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603062	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614832	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs616085	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs624786	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs625268	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs629573	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs641584	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs643807	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs646287	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688665	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[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	nsv932190	chr11:74359867-74618935	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
2	nsv832210	chr11:74562782-74732133	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs557483	RP11-147I3.1	cis	Thyroid	GTEx
rs557483	XRRA1	cis	Artery Tibial	GTEx
rs557483	XRRA1	cis	Thyroid	GTEx
rs557483	XRRA1	cis	Whole Blood	GTEx
rs557483	XRRA1	cis	Muscle Skeletal	GTEx
rs557483	XRRA1	cis	lung	GTEx
rs557483	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs557483	XRRA1	cis	Esophagus Mucosa	GTEx
rs557483	XRRA1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74587400-74629600	Weak transcription	Gastric	stomach
2	chr11:74588400-74630600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr11:74588400-74636000	Weak transcription	NHLF	lung
4	chr11:74594800-74646600	Weak transcription	Small Intestine	intestine
5	chr11:74596800-74619000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr11:74598200-74615200	Weak transcription	Osteobl	bone
7	chr11:74598400-74629600	Weak transcription	Colon Smooth Muscle	Colon
8	chr11:74599200-74619400	Weak transcription	Colonic Mucosa	Colon
9	chr11:74603200-74617800	Weak transcription	K562	blood
10	chr11:74603800-74616600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr11:74606600-74626400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:74606800-74616200	Weak transcription	NHEK	skin
13	chr11:74607200-74618000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:74607400-74617200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr11:74607600-74616400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr11:74607600-74616600	Weak transcription	Placenta	Placenta
17	chr11:74607600-74617200	Weak transcription	Thymus	Thymus
18	chr11:74607600-74618200	Weak transcription	Hela-S3	cervix
19	chr11:74607600-74637400	Weak transcription	Pancreas	Pancrea
20	chr11:74607800-74616200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr11:74607800-74616200	Weak transcription	Aorta	Aorta
22	chr11:74607800-74616400	Weak transcription	Primary T cells from cord blood	blood
23	chr11:74607800-74616400	Weak transcription	Left Ventricle	heart
24	chr11:74607800-74616400	Weak transcription	Lung	lung
25	chr11:74607800-74616600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:74607800-74618000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:74607800-74618000	Weak transcription	Ovary	ovary
28	chr11:74607800-74620800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:74608000-74616600	Weak transcription	HepG2	liver
30	chr11:74608000-74618000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr11:74611600-74615800	Weak transcription	HUVEC	blood vessel
32	chr11:74611600-74616000	Weak transcription	Fetal Stomach	stomach
33	chr11:74612200-74615600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:74612200-74616400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr11:74612200-74620600	Weak transcription	HSMM	muscle
36	chr11:74612400-74629600	Weak transcription	NHDF-Ad	bronchial
37	chr11:74612600-74617000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr11:74612800-74615600	Weak transcription	Dnd41	blood
39	chr11:74612800-74616000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:74612800-74616400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr11:74612800-74617000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:74612800-74618200	Weak transcription	Brain Hippocampus Middle	brain
43	chr11:74612800-74619000	Weak transcription	Brain Angular Gyrus	brain
44	chr11:74612800-74621200	Weak transcription	Fetal Kidney	kidney
45	chr11:74612800-74634000	Weak transcription	Psoas Muscle	Psoas
46	chr11:74613000-74616200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr11:74613000-74616600	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr11:74613000-74616800	Weak transcription	Rectal Smooth Muscle	rectum
49	chr11:74613000-74620200	Weak transcription	Fetal Heart	heart
50	chr11:74613400-74621000	Weak transcription	Brain Substantia Nigra	brain

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