Variant report

Variant	rs59328242
Chromosome Location	chr11:74580965-74580966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:74575930..74578650-chr11:74579963..74582889,3	K562	blood:
2	chr11:74576667..74578620-chr11:74579623..74581389,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF169-2	chr11:74580963-74581071	NONHSAT022959

Extended variants
information (count: 49 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10160410	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10751241	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10793105	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10793107	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10793108	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10899045	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10899051	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10899052	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11236244	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12221841	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12225372	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12225387	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12419113	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12419929	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12421899	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12574850	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12575200	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576129	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12577614	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17133461	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2119028	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2165162	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2165163	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2298746	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2304683	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3814726	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4483614	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4944061	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4944950	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4944960	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944961	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944963	0.86[AMR][1000 genomes]
rs59143825	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61671395	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61734374	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61894779	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61894839	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7102619	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7105085	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7128739	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs725460	0.82[AMR][1000 genomes]
rs7396866	0.83[AMR][1000 genomes]
rs7928381	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs919877	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9787775	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9787897	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs59328242	XRRA1	cis	Artery Aorta	GTEx
rs59328242	XRRA1	cis	lung	GTEx
rs59328242	XRRA1	cis	Whole Blood	GTEx
rs59328242	XRRA1	cis	Thyroid	GTEx
rs59328242	RP11-147I3.1	cis	lung	GTEx
rs59328242	XRRA1	cis	Nerve Tibial	GTEx
rs59328242	XRRA1	cis	Artery Tibial	GTEx
rs59328242	XRRA1	cis	Esophagus Mucosa	GTEx
rs59328242	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs59328242	XRRA1	cis	Esophagus Muscularis	GTEx
rs59328242	XRRA1	cis	Adipose Subcutaneous	GTEx
rs59328242	RP11-147I3.1	cis	Esophagus Muscularis	GTEx
rs59328242	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs59328242	RP11-147I3.1	cis	Thyroid	GTEx
rs59328242	XRRA1	cis	Heart Left Ventricle	GTEx
rs59328242	XRRA1	cis	Muscle Skeletal	GTEx
rs59328242	XRRA1	cis	Stomach	GTEx
rs59328242	XRRA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74562200-74595800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:74569800-74588400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr11:74570000-74588400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:74570600-74585600	ZNF genes & repeats	Dnd41	blood
5	chr11:74570600-74588400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr11:74570800-74584800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr11:74571000-74588400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr11:74571200-74584400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:74571200-74585200	ZNF genes & repeats	Brain Germinal Matrix	brain
10	chr11:74573600-74588400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr11:74574200-74588400	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr11:74574800-74586600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
13	chr11:74575400-74584600	ZNF genes & repeats	Brain Substantia Nigra	brain
14	chr11:74575600-74584200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr11:74575600-74584400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:74575600-74584800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
17	chr11:74575600-74585000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
18	chr11:74575600-74585800	ZNF genes & repeats	Fetal Intestine Large	intestine
19	chr11:74575600-74588400	ZNF genes & repeats	Liver	Liver
20	chr11:74575800-74584000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
21	chr11:74576000-74583800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
22	chr11:74576200-74581000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr11:74576200-74586600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
24	chr11:74576400-74583800	ZNF genes & repeats	Brain Anterior Caudate	brain
25	chr11:74576400-74583800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
26	chr11:74576600-74584600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr11:74576600-74585000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
28	chr11:74577400-74581600	Weak transcription	HMEC	breast
29	chr11:74578200-74581800	Weak transcription	K562	blood
30	chr11:74578200-74582200	Weak transcription	Pancreas	Pancrea
31	chr11:74578400-74582200	Weak transcription	NHLF	lung
32	chr11:74578800-74581200	Weak transcription	A549	lung
33	chr11:74578800-74581800	Weak transcription	Osteobl	bone
34	chr11:74579200-74581200	Weak transcription	HSMM	muscle
35	chr11:74579400-74587800	ZNF genes & repeats	Fetal Brain Female	brain
36	chr11:74579400-74588000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr11:74579800-74581000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr11:74579800-74581800	Weak transcription	HepG2	liver
39	chr11:74580000-74581000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:74580000-74581000	Weak transcription	Fetal Lung	lung
41	chr11:74580000-74582200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr11:74580200-74581200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr11:74580200-74582000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:74580200-74584400	ZNF genes & repeats	Placenta	Placenta
45	chr11:74580400-74582800	ZNF genes & repeats	Small Intestine	intestine
46	chr11:74580400-74583400	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:74580400-74583600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
48	chr11:74580400-74584200	ZNF genes & repeats	Brain Hippocampus Middle	brain
49	chr11:74580400-74584200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
50	chr11:74580400-74584600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin

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