Variant report

Variant	rs12419113
Chromosome Location	chr11:74579749-74579750
allele	A/C
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	SETDB1	chr11:74579071-74579892	U2OS	brain:	n/a	n/a

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

Variant related genes	Relation type
XRRA1	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10160410	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10751241	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10793105	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10793107	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10793108	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10899045	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10899051	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899052	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10899054	0.81[AMR][1000 genomes]
rs11236244	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11236282	0.81[AMR][1000 genomes]
rs11236290	0.81[AMR][1000 genomes]
rs11603294	0.81[AMR][1000 genomes]
rs12221841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12225372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12225387	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12419929	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12421899	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12574850	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12575200	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12576129	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12577127	0.81[AMR][1000 genomes]
rs12577614	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17133461	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2119028	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2165162	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2165163	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2298746	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304683	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3814726	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4387374	0.81[AMR][1000 genomes]
rs4483614	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4944061	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4944950	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4944960	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944961	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4944963	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4944965	0.82[AMR][1000 genomes]
rs4944968	0.81[AMR][1000 genomes]
rs56194145	0.82[AMR][1000 genomes]
rs59143825	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59328242	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61671395	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61734374	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61894779	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61894839	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7102619	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7105085	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7128739	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs725460	0.85[AMR][1000 genomes]
rs7396866	0.82[AMR][1000 genomes]
rs7928381	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs919877	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9787775	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9787897	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs12419113	XRRA1	cis	Stomach	GTEx
rs12419113	XRRA1	cis	Nerve Tibial	GTEx
rs12419113	XRRA1	cis	Artery Aorta	GTEx
rs12419113	XRRA1	cis	Thyroid	GTEx
rs12419113	XRRA1	cis	lung	GTEx
rs12419113	XRRA1	cis	Muscle Skeletal	GTEx
rs12419113	RP11-147I3.1	cis	Muscle Skeletal	GTEx
rs12419113	XRRA1	cis	Esophagus Mucosa	GTEx
rs12419113	RP11-147I3.1	cis	Thyroid	GTEx
rs12419113	XRRA1	cis	Heart Left Ventricle	GTEx
rs12419113	XRRA1	cis	Artery Tibial	GTEx
rs12419113	RP11-147I3.1	cis	Esophagus Muscularis	GTEx
rs12419113	XRRA1	cis	Skin Sun Exposed Lower leg	GTEx
rs12419113	XRRA1	cis	Esophagus Muscularis	GTEx
rs12419113	XRRA1	cis	Whole Blood	GTEx
rs12419113	XRRA1	cis	Adipose Subcutaneous	GTEx
rs12419113	XRRA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 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	chr11:74570800-74579800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
7	chr11:74570800-74584800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:74571000-74588400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
9	chr11:74571200-74584400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr11:74571200-74585200	ZNF genes & repeats	Brain Germinal Matrix	brain
11	chr11:74573600-74588400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:74574200-74588400	ZNF genes & repeats	Adipose Nuclei	Adipose
13	chr11:74574800-74586600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
14	chr11:74575400-74584600	ZNF genes & repeats	Brain Substantia Nigra	brain
15	chr11:74575600-74580400	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
16	chr11:74575600-74584200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr11:74575600-74584400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr11:74575600-74584800	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
19	chr11:74575600-74585000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
20	chr11:74575600-74585800	ZNF genes & repeats	Fetal Intestine Large	intestine
21	chr11:74575600-74588400	ZNF genes & repeats	Liver	Liver
22	chr11:74575800-74584000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
23	chr11:74576000-74583800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
24	chr11:74576200-74581000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:74576200-74586600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
26	chr11:74576400-74580000	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr11:74576400-74583800	ZNF genes & repeats	Brain Anterior Caudate	brain
28	chr11:74576400-74583800	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
29	chr11:74576600-74580200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
30	chr11:74576600-74584600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr11:74576600-74585000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
32	chr11:74576800-74580200	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
33	chr11:74577400-74581600	Weak transcription	HMEC	breast
34	chr11:74577800-74579800	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
35	chr11:74578200-74580600	Weak transcription	Esophagus	oesophagus
36	chr11:74578200-74581800	Weak transcription	K562	blood
37	chr11:74578200-74582200	Weak transcription	Pancreas	Pancrea
38	chr11:74578400-74580600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr11:74578400-74582200	Weak transcription	NHLF	lung
40	chr11:74578800-74580600	Weak transcription	NHEK	skin
41	chr11:74578800-74581200	Weak transcription	A549	lung
42	chr11:74578800-74581800	Weak transcription	Osteobl	bone
43	chr11:74579200-74580000	ZNF genes & repeats	Fetal Lung	lung
44	chr11:74579200-74581200	Weak transcription	HSMM	muscle
45	chr11:74579400-74579800	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:74579400-74579800	ZNF genes & repeats	HepG2	liver
47	chr11:74579400-74580200	Weak transcription	Placenta	Placenta
48	chr11:74579400-74580400	Weak transcription	Fetal Intestine Small	intestine
49	chr11:74579400-74580400	Weak transcription	Small Intestine	intestine
50	chr11:74579400-74580600	Weak transcription	Left Ventricle	heart

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