Variant report

Variant	rs529249
Chromosome Location	chr11:74630253-74630254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:74630240-74630390	GM06990	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74624254..74626945-chr11:74627904..74632353,5	K562	blood:

Variant related genes	Relation type
ENSG00000241170	TF binding region
ENSG00000241170	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11236269	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11605604	0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12363224	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1282460	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1282461	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1282689	0.94[ASN][1000 genomes]
rs1282690	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1282692	0.88[ASN][1000 genomes]
rs1282695	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1292895	0.94[ASN][1000 genomes]
rs1297319	0.92[ASN][1000 genomes]
rs1303525	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1315297	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1583342	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2028343	0.92[ASN][1000 genomes]
rs2028344	0.92[ASN][1000 genomes]
rs2033532	0.88[AMR][1000 genomes]
rs41531051	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs471462	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs473080	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs473256	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480840	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs483615	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs495246	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs502225	0.83[AMR][1000 genomes]
rs505688	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs508319	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs511021	0.92[ASN][1000 genomes]
rs511890	0.92[ASN][1000 genomes]
rs512780	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs513137	0.86[AMR][1000 genomes]
rs519741	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs527529	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529488	0.92[ASN][1000 genomes]
rs537054	0.87[ASN][1000 genomes]
rs538502	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs543244	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs546643	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs550491	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550869	0.92[ASN][1000 genomes]
rs550980	0.98[ASN][1000 genomes]
rs557483	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs561589	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs562265	0.94[ASN][1000 genomes]
rs565767	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs567956	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs568558	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs568758	0.92[ASN][1000 genomes]
rs571446	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs573925	1.00[ASN][1000 genomes]
rs577063	0.88[ASN][1000 genomes]
rs577102	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs580142	0.83[AMR][1000 genomes]
rs590105	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599722	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs603062	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614832	0.94[ASN][1000 genomes]
rs616085	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs624786	0.87[ASN][1000 genomes]
rs625268	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs629573	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs641584	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs643807	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs646287	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs688665	0.94[ASN][1000 genomes]
rs9444	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs997465	0.81[AMR][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	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
2	nsv972046	chr11:74629931-74632251	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs529249	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs529249	XRRA1	cis	Whole Blood	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74588400-74630600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr11:74588400-74636000	Weak transcription	NHLF	lung
3	chr11:74594800-74646600	Weak transcription	Small Intestine	intestine
4	chr11:74607600-74637400	Weak transcription	Pancreas	Pancrea
5	chr11:74612800-74634000	Weak transcription	Psoas Muscle	Psoas
6	chr11:74613400-74632600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:74613800-74637400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr11:74614600-74633600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr11:74615000-74636200	Weak transcription	A549	lung
10	chr11:74615200-74632600	Strong transcription	Liver	Liver
11	chr11:74615200-74637200	Weak transcription	HMEC	breast
12	chr11:74615800-74633600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:74615800-74644800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr11:74616000-74634200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr11:74616000-74634800	Strong transcription	Fetal Intestine Large	intestine
16	chr11:74616200-74634000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:74616400-74633600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr11:74616400-74634400	Strong transcription	Primary T cells from cord blood	blood
19	chr11:74616400-74646000	Weak transcription	Spleen	Spleen
20	chr11:74616400-74656200	Weak transcription	Stomach Mucosa	stomach
21	chr11:74616600-74632600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr11:74616600-74632600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr11:74617000-74631800	Weak transcription	HUVEC	blood vessel
24	chr11:74617200-74635200	Strong transcription	Fetal Muscle Trunk	muscle
25	chr11:74617400-74648200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:74618000-74659600	Weak transcription	Esophagus	oesophagus
27	chr11:74618400-74653800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr11:74619200-74639800	Weak transcription	K562	blood
29	chr11:74620000-74646200	Weak transcription	Right Ventricle	heart
30	chr11:74620400-74659600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr11:74620600-74631600	Weak transcription	Fetal Heart	heart
32	chr11:74621200-74634800	Strong transcription	Primary B cells from cord blood	blood
33	chr11:74622400-74633000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr11:74622800-74633000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:74623800-74632400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr11:74624200-74643200	Weak transcription	HSMMtube	muscle
37	chr11:74624600-74632400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr11:74624600-74632800	Strong transcription	Thymus	Thymus
39	chr11:74625400-74633000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr11:74625400-74634200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr11:74625600-74632200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:74625600-74633000	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr11:74625800-74630800	Strong transcription	Fetal Lung	lung
44	chr11:74625800-74633000	Strong transcription	Ovary	ovary
45	chr11:74625800-74633400	Strong transcription	Fetal Muscle Leg	muscle
46	chr11:74626000-74632200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:74626000-74632400	Strong transcription	Adipose Nuclei	Adipose
48	chr11:74626200-74632800	Strong transcription	Placenta	Placenta
49	chr11:74626200-74633000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr11:74626400-74632200	Strong transcription	HUES64 Cell Line	embryonic stem cell

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