Variant report

Variant	rs12309824
Chromosome Location	chr12:120990582-120990583
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr12:120990495-120990876	MCF-7	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120972092..120974371-chr12:120989548..120992065,2	K562	blood:
2	chr12:120990509..120992158-chr12:120997658..120999306,2	MCF-7	breast:
3	chr12:120966448..120968669-chr12:120990053..120993175,3	MCF-7	breast:
4	chr12:120982785..120987053-chr12:120988717..120992540,5	MCF-7	breast:
5	chr12:120982370..120986191-chr12:120990238..120994001,4	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DYNLL1-2	chr12:120990578-120991120	l_746_chr12:120985636-120987727_prostate

No data

Variant related genes	Relation type
RNF10	TF binding region
ENSG00000110871	Chromatin interaction
ENSG00000022840	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs1048830	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1050187	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10744752	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10774549	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10774551	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10774553	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10774555	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10774560	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10774561	0.85[EUR][1000 genomes]
rs10849753	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10849754	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849757	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10849758	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10849759	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10849766	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10849767	0.84[EUR][1000 genomes]
rs11065132	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11065145	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11065149	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11065150	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11065151	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11065154	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12312613	0.84[EUR][1000 genomes]
rs12370495	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12371550	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12813930	0.92[ASN][1000 genomes]
rs12814055	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1563333	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2138251	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2168319	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2233676	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2235217	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2235218	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2393590	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3213565	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3742052	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3759394	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3759396	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3893104	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3916065	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766966	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4766968	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4766969	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4767897	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4767902	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4767903	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767904	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4767905	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767906	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4767910	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4767911	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4767912	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4767914	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4767916	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs509445	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs516479	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs523522	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs524735	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs546417	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55848094	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56029862	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs579919	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs585510	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs603574	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61945857	0.90[AMR][1000 genomes]
rs643372	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs651627	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs655530	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs670568	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs687873	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7136951	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71454645	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7308053	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7471	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7488320	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9040	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9788155	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9795621	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv906	chr12:120973683-121018441	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12309824	COQ5	cis	Skin Sun Exposed Lower leg	GTEx
rs12309824	COQ5	cis	Artery Tibial	GTEx
rs12309824	COQ5	cis	Adipose Subcutaneous	GTEx
rs12309824	COQ5	cis	Nerve Tibial	GTEx
rs12309824	COQ5	cis	lung	GTEx
rs12309824	COQ5	Cis_1M	lymphoblastoid	RTeQTL
rs12309824	COQ5	cis	Muscle Skeletal	GTEx
rs12309824	COQ5	cis	Artery Aorta	GTEx
rs12309824	COQ5	cis	Esophagus Muscularis	GTEx
rs12309824	COQ5	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120976000-121018000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:120976400-121018200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:120977400-120995600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:120977400-121017600	Strong transcription	Fetal Thymus	thymus
5	chr12:120977400-121018200	Strong transcription	Fetal Stomach	stomach
6	chr12:120977600-121016800	Strong transcription	Dnd41	blood
7	chr12:120982200-121017600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:120983600-121017600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr12:120983600-121017600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr12:120983600-121017800	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:120983600-121017800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:120983600-121017800	Strong transcription	Fetal Muscle Trunk	muscle
13	chr12:120983800-121017800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:120983800-121017800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:120984000-120995000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:120984000-120996000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:120984000-121017800	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr12:120984000-121017800	Strong transcription	Fetal Intestine Large	intestine
19	chr12:120984000-121017800	Strong transcription	Thymus	Thymus
20	chr12:120984000-121018200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:120984200-120996000	Strong transcription	Placenta Amnion	Placenta Amnion
22	chr12:120984200-121017400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:120984400-120996800	Strong transcription	Fetal Brain Female	brain
24	chr12:120984400-121018000	Strong transcription	Brain Germinal Matrix	brain
25	chr12:120984600-120992000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:120984800-120995600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:120985600-120992000	Weak transcription	Aorta	Aorta
28	chr12:120985600-121000800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:120985600-121018200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:120985800-120992200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:120985800-120992400	Weak transcription	Fetal Heart	heart
32	chr12:120986600-120990600	Genic enhancers	Left Ventricle	heart
33	chr12:120986600-120992200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:120986600-120992200	Weak transcription	Fetal Brain Male	brain
35	chr12:120986600-120992200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr12:120987000-120990800	Genic enhancers	Duodenum Mucosa	Duodenum
37	chr12:120987000-120990800	Genic enhancers	Rectal Mucosa Donor 29	rectum
38	chr12:120987200-120992000	Weak transcription	HMEC	breast
39	chr12:120987200-120992200	Weak transcription	Colon Smooth Muscle	Colon
40	chr12:120987400-120991600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr12:120987400-120992000	Weak transcription	Esophagus	oesophagus
42	chr12:120987400-120992000	Weak transcription	Gastric	stomach
43	chr12:120987400-120992000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr12:120987400-120992200	Weak transcription	Psoas Muscle	Psoas
45	chr12:120988200-120992200	Weak transcription	Right Ventricle	heart
46	chr12:120988200-120995000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr12:120988200-120995600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr12:120988200-121017800	Strong transcription	Stomach Smooth Muscle	stomach
49	chr12:120988200-121018200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr12:120988400-120990600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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