Variant report

Variant	rs573925
Chromosome Location	chr11:74642446-74642447
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74640923..74643300-chr11:74745536..74747928,2	K562	blood:
2	chr11:74640377..74642514-chr11:74652092..74654099,2	K562	blood:
3	chr11:74640134..74643076-chr11:74654287..74656297,2	MCF-7	breast:
4	chr11:74631923..74634121-chr11:74641011..74642519,2	K562	blood:
5	chr11:74641794..74643776-chr11:74964024..74966770,2	K562	blood:
6	chr11:74642326..74645440-chr11:74646837..74649295,3	K562	blood:
7	chr11:74641314..74643674-chr11:74698479..74700566,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162139	Chromatin interaction
ENSG00000166435	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11236269	1.00[ASN][1000 genomes]
rs11605604	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12363224	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1282460	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1282461	0.85[ASN][1000 genomes]
rs1282689	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1282690	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1282692	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1282695	0.92[ASN][1000 genomes]
rs1292895	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1297319	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1315297	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1583342	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2028343	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2028344	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2033532	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41531051	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs471462	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs473080	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs473256	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs480840	1.00[ASN][1000 genomes]
rs495246	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs502225	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs508319	0.98[ASN][1000 genomes]
rs511021	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs511890	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs513137	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs519741	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs527529	1.00[ASN][1000 genomes]
rs529249	1.00[ASN][1000 genomes]
rs529488	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs537054	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs538502	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs543244	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs546643	0.94[ASN][1000 genomes]
rs550491	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550869	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550980	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs557483	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs562265	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs567956	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs568558	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs568758	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs571446	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs577063	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs580142	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs590105	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599722	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs603062	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs614832	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs616085	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs624786	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs625268	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs629573	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs641584	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs643807	0.94[ASN][1000 genomes]
rs646287	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs688665	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9444	0.90[AMR][1000 genomes];0.93[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	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	esv3346818	chr11:74642445-74642638	Strong transcription Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs573925	XRRA1	cis	Esophagus Mucosa	GTEx
rs573925	XRRA1	cis	Nerve Tibial	GTEx
rs573925	XRRA1	cis	lung	GTEx
rs573925	XRRA1	cis	Thyroid	GTEx
rs573925	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs573925	XRRA1	cis	Muscle Skeletal	GTEx
rs573925	XRRA1	cis	Adipose Subcutaneous	GTEx
rs573925	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs573925	XRRA1	cis	Whole Blood	GTEx
rs573925	RP11-147I3.1	cis	Thyroid	GTEx
rs573925	XRRA1	cis	Artery Tibial	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74594800-74646600	Weak transcription	Small Intestine	intestine
2	chr11:74615800-74644800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr11:74616400-74646000	Weak transcription	Spleen	Spleen
4	chr11:74616400-74656200	Weak transcription	Stomach Mucosa	stomach
5	chr11:74617400-74648200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr11:74618000-74659600	Weak transcription	Esophagus	oesophagus
7	chr11:74618400-74653800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr11:74620000-74646200	Weak transcription	Right Ventricle	heart
9	chr11:74620400-74659600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr11:74624200-74643200	Weak transcription	HSMMtube	muscle
11	chr11:74627800-74659200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr11:74628200-74659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:74630000-74643400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:74630000-74645200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr11:74630000-74646000	Weak transcription	Aorta	Aorta
16	chr11:74630200-74643400	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr11:74630400-74644600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr11:74630800-74646000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:74630800-74659000	Weak transcription	Fetal Brain Male	brain
20	chr11:74631000-74646000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr11:74631600-74659000	Weak transcription	Hela-S3	cervix
22	chr11:74632200-74643400	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr11:74632200-74644000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:74632200-74646000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr11:74632200-74659600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr11:74632400-74643200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr11:74632400-74643400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr11:74632400-74643400	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr11:74632400-74643600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr11:74632400-74644200	Weak transcription	Fetal Thymus	thymus
31	chr11:74632400-74644800	Weak transcription	Fetal Brain Female	brain
32	chr11:74632400-74645600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr11:74632400-74646000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr11:74632400-74646000	Weak transcription	Brain Germinal Matrix	brain
35	chr11:74632400-74647200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:74632400-74647200	Weak transcription	Lung	lung
37	chr11:74632400-74648400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr11:74632600-74644400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr11:74633000-74643400	Weak transcription	Brain Hippocampus Middle	brain
40	chr11:74633000-74643400	Weak transcription	Fetal Kidney	kidney
41	chr11:74633000-74643400	Weak transcription	Ovary	ovary
42	chr11:74633000-74643800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr11:74633000-74645600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:74633000-74659400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr11:74634200-74646200	Weak transcription	Gastric	stomach
46	chr11:74634400-74646600	Weak transcription	Psoas Muscle	Psoas
47	chr11:74634600-74642800	Weak transcription	Adipose Nuclei	Adipose
48	chr11:74634600-74643400	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr11:74634600-74643400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr11:74634800-74644000	Weak transcription	Primary B cells from cord blood	blood

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