Variant report

Variant	rs550491
Chromosome Location	chr11:74621021-74621022
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs11236269	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11605604	1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12363224	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1282460	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1282461	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1282689	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1282690	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1282692	1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1282695	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1292895	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1297319	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1303525	0.81[AMR][1000 genomes]
rs1315297	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1583342	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2028343	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2028344	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2033532	0.89[CHB][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2919057	1.00[CHB][hapmap]
rs41531051	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs471462	1.00[CHB][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs473080	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs473256	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs480840	1.00[CHB][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs483615	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4944945	0.88[YRI][hapmap]
rs495246	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs497772	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs502225	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs505688	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs508319	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs511021	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs511890	1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs512780	0.88[CHB][hapmap];0.88[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs513137	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs519741	1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs527529	1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529249	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529488	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs537054	1.00[CHB][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs538502	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs543244	1.00[CHB][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs546643	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs550869	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs550980	0.89[CHB][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557483	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs561589	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs562265	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs565767	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs567956	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs568558	1.00[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568758	0.88[CHB][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs571446	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs573925	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs577063	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs577102	1.00[CHB][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes]
rs580142	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs590105	1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs599722	1.00[CHB][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs603062	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs614832	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs616085	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs624786	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs625268	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs629573	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs641584	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs643807	1.00[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs646287	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs688665	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9444	0.87[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs997465	1.00[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs550491	XRRA1	cis	Artery Tibial	GTEx
rs550491	XRRA1	cis	Muscle Skeletal	GTEx
rs550491	XRRA1	cis	Thyroid	GTEx
rs550491	XRRA1	cis	Esophagus Mucosa	GTEx
rs550491	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs550491	XRRA1	cis	Adipose Subcutaneous	GTEx
rs550491	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs550491	XRRA1	cis	lung	GTEx
rs550491	RP11-147I3.1	cis	Thyroid	GTEx
rs550491	XRRA1	cis	Whole Blood	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

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	chr11:74598400-74629600	Weak transcription	Colon Smooth Muscle	Colon
6	chr11:74606600-74626400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:74607600-74637400	Weak transcription	Pancreas	Pancrea
8	chr11:74612400-74629600	Weak transcription	NHDF-Ad	bronchial
9	chr11:74612800-74621200	Weak transcription	Fetal Kidney	kidney
10	chr11:74612800-74634000	Weak transcription	Psoas Muscle	Psoas
11	chr11:74613400-74632600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr11:74613600-74624000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:74613600-74627800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:74613800-74628600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:74613800-74637400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr11:74614400-74623000	Strong transcription	Fetal Intestine Small	intestine
17	chr11:74614600-74633600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr11:74615000-74629600	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:74615000-74629600	Weak transcription	NH-A	brain
20	chr11:74615000-74636200	Weak transcription	A549	lung
21	chr11:74615200-74632600	Strong transcription	Liver	Liver
22	chr11:74615200-74637200	Weak transcription	HMEC	breast
23	chr11:74615400-74623600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr11:74615400-74626400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr11:74615600-74626600	Strong transcription	Dnd41	blood
26	chr11:74615800-74633600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr11:74615800-74644800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr11:74616000-74621200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr11:74616000-74622800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr11:74616000-74634200	Strong transcription	Duodenum Mucosa	Duodenum
31	chr11:74616000-74634800	Strong transcription	Fetal Intestine Large	intestine
32	chr11:74616200-74626800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:74616200-74634000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr11:74616400-74621400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr11:74616400-74622200	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr11:74616400-74623600	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr11:74616400-74633600	Strong transcription	Stomach Smooth Muscle	stomach
38	chr11:74616400-74634400	Strong transcription	Primary T cells from cord blood	blood
39	chr11:74616400-74646000	Weak transcription	Spleen	Spleen
40	chr11:74616400-74656200	Weak transcription	Stomach Mucosa	stomach
41	chr11:74616600-74622200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr11:74616600-74622400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr11:74616600-74623200	Strong transcription	Adipose Nuclei	Adipose
44	chr11:74616600-74623400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr11:74616600-74629200	Weak transcription	Fetal Thymus	thymus
46	chr11:74616600-74632600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr11:74616600-74632600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr11:74616800-74621400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr11:74616800-74622400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr11:74617000-74622200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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