Variant report

Variant	rs580142
Chromosome Location	chr11:74485926-74485927
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:74459784..74462637-chr11:74484439..74486844,2	MCF-7	breast:
2	chr11:74485370..74487862-chr11:74489237..74491586,3	K562	blood:
3	chr11:74482976..74485949-chr11:74491370..74492994,2	MCF-7	breast:
4	chr11:74463706..74466007-chr11:74485588..74487545,2	K562	blood:

Variant related genes	Relation type
ENSG00000166439	Chromatin interaction
ENSG00000264095	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11236269	0.83[AMR][1000 genomes]
rs11605604	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12363224	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1282460	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1282461	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1282689	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1282690	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1282692	0.84[EUR][1000 genomes]
rs1292895	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1297319	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1303525	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1315297	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1583342	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2028343	0.84[EUR][1000 genomes]
rs2028344	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2033532	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41531051	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs471462	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs473080	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs473256	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs480840	0.81[AFR][1000 genomes]
rs483615	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4944945	0.82[AFR][1000 genomes]
rs495246	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs497772	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs502225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs505688	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs508319	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs511021	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs511890	0.86[EUR][1000 genomes]
rs512780	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs513137	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs519741	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs527529	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs529249	0.83[AMR][1000 genomes]
rs529488	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs537054	0.84[EUR][1000 genomes]
rs538502	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs543244	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs546643	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs550491	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs550869	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs557483	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs561589	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs562265	0.82[EUR][1000 genomes]
rs565767	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs567956	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs568558	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs568758	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs571446	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs573925	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs577063	0.80[EUR][1000 genomes]
rs577102	0.99[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs590105	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs599722	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs603062	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs614832	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs616085	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs624786	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs625268	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs629573	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs641584	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs643807	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs646287	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs688665	0.85[EUR][1000 genomes]
rs9444	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	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
7	esv1840811	chr11:74452658-74488369	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
8	nsv897916	chr11:74465068-74574677	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv897917	chr11:74474266-74595507	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs580142	XRRA1	cis	lung	GTEx
rs580142	XRRA1	cis	Thyroid	GTEx
rs580142	XRRA1	cis	Adipose Subcutaneous	GTEx
rs580142	XRRA1	cis	Whole Blood	GTEx
rs580142	XRRA1	cis	Artery Tibial	GTEx
rs580142	RP11-147I3.1	cis	Thyroid	GTEx
rs580142	XRRA1	Cis_1M	lymphoblastoid	RTeQTL
rs580142	XRRA1	cis	Muscle Skeletal	GTEx
rs580142	XRRA1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74461600-74494000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr11:74462600-74487800	Weak transcription	K562	blood
3	chr11:74467000-74494200	Weak transcription	Hela-S3	cervix
4	chr11:74467200-74490800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr11:74467200-74493200	Weak transcription	Pancreas	Pancrea
6	chr11:74467400-74486000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr11:74467800-74489000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:74468000-74494000	Weak transcription	Dnd41	blood
9	chr11:74468000-74500800	Weak transcription	HepG2	liver
10	chr11:74470400-74494000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:74470600-74500800	Weak transcription	Fetal Muscle Leg	muscle
12	chr11:74475200-74491200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr11:74475400-74494600	Weak transcription	Esophagus	oesophagus
14	chr11:74475600-74489000	Weak transcription	Left Ventricle	heart
15	chr11:74476200-74493400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:74476200-74494400	Weak transcription	Fetal Stomach	stomach
17	chr11:74476600-74493200	Weak transcription	Right Atrium	heart
18	chr11:74477400-74487800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:74478000-74501600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr11:74479000-74489000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:74479800-74488400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr11:74480200-74501400	Weak transcription	Fetal Intestine Small	intestine
23	chr11:74481200-74488400	Weak transcription	Lung	lung
24	chr11:74481200-74490800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr11:74481200-74492800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr11:74481400-74487800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr11:74481400-74494600	Weak transcription	Small Intestine	intestine
28	chr11:74481600-74490800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:74481600-74493400	Weak transcription	HSMM	muscle
30	chr11:74481600-74493800	Weak transcription	Primary hematopoietic stem cells	blood
31	chr11:74481800-74488000	Weak transcription	Primary B cells from cord blood	blood
32	chr11:74481800-74488400	Weak transcription	Primary T cells from cord blood	blood
33	chr11:74481800-74492800	Weak transcription	NHEK	skin
34	chr11:74481800-74493800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:74481800-74494000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:74482000-74486800	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr11:74482200-74486800	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr11:74482200-74490000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr11:74482200-74490800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr11:74482200-74492000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr11:74482200-74493200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr11:74482400-74487400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr11:74482400-74493200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr11:74482800-74492000	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr11:74483800-74487600	Weak transcription	Brain Hippocampus Middle	brain
46	chr11:74483800-74497600	Weak transcription	Fetal Heart	heart
47	chr11:74484000-74486000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:74484200-74486000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr11:74484200-74489800	Weak transcription	GM12878-XiMat	blood
50	chr11:74484400-74487400	Enhancers	Muscle Satellite Cultured Cells	--

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