Variant report

Variant	rs62280667
Chromosome Location	chr3:101084604-101084605
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10936607	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936664	0.88[ASN][1000 genomes]
rs12491955	0.90[ASN][1000 genomes]
rs12496260	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13062095	0.88[EUR][1000 genomes]
rs13087404	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13088318	0.93[EUR][1000 genomes]
rs13089177	0.81[ASN][1000 genomes]
rs13089552	0.86[ASN][1000 genomes]
rs13320918	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2141179	0.86[ASN][1000 genomes]
rs2141180	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2178036	0.82[ASN][1000 genomes]
rs2250611	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317699	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317700	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2317745	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317749	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2317751	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2433031	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553416	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553424	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2553427	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2553430	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2682383	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2682384	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682386	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682390	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682391	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28565548	0.81[ASN][1000 genomes]
rs34255148	0.82[ASN][1000 genomes]
rs348866	0.83[ASN][1000 genomes]
rs348869	0.84[ASN][1000 genomes]
rs3846091	0.88[ASN][1000 genomes]
rs4456838	0.81[ASN][1000 genomes]
rs4524254	0.81[ASN][1000 genomes]
rs4683899	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683900	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4683917	0.91[ASN][1000 genomes]
rs4683918	0.87[ASN][1000 genomes]
rs473702	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs497953	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503734	0.89[ASN][1000 genomes]
rs508537	0.86[ASN][1000 genomes]
rs520558	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533852	0.84[ASN][1000 genomes]
rs551442	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075912	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441602	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441608	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6441610	0.84[ASN][1000 genomes]
rs6771561	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6773536	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636475	0.84[ASN][1000 genomes]
rs9843186	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9856435	0.88[ASN][1000 genomes]
rs9859077	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870114	0.81[ASN][1000 genomes]
rs9874188	0.84[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	nsv931417	chr3:100547347-101183844	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv3439278	chr3:100936513-101162102	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1003475	chr3:101005238-101120030	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62280667	SENP7	cis	Nerve Tibial	GTEx
rs62280667	SENP7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101030800-101096400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:101038600-101101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr3:101038800-101089800	Weak transcription	Pancreas	Pancrea
4	chr3:101039800-101106600	Weak transcription	Thymus	Thymus
5	chr3:101040600-101086800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:101040800-101090000	Weak transcription	Brain Angular Gyrus	brain
7	chr3:101042800-101089600	Weak transcription	NH-A	brain
8	chr3:101043200-101105000	Weak transcription	Brain Anterior Caudate	brain
9	chr3:101043800-101096600	Weak transcription	Brain Substantia Nigra	brain
10	chr3:101044400-101103000	Weak transcription	Gastric	stomach
11	chr3:101045800-101110800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:101046400-101089000	Weak transcription	Fetal Brain Male	brain
13	chr3:101047400-101096000	Weak transcription	Psoas Muscle	Psoas
14	chr3:101048600-101088000	Weak transcription	HUVEC	blood vessel
15	chr3:101049200-101096000	Weak transcription	Ovary	ovary
16	chr3:101049200-101102200	Weak transcription	Right Ventricle	heart
17	chr3:101054600-101085000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:101066000-101089800	Weak transcription	Brain Germinal Matrix	brain
19	chr3:101066000-101094000	Weak transcription	Fetal Intestine Large	intestine
20	chr3:101066200-101089000	Weak transcription	Fetal Lung	lung
21	chr3:101066200-101095400	Weak transcription	Fetal Kidney	kidney
22	chr3:101066200-101096000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:101066400-101085000	Weak transcription	Placenta	Placenta
24	chr3:101069000-101089800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:101073200-101091000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:101074600-101092200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:101075000-101085600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:101076000-101085600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr3:101076000-101088000	Weak transcription	NHLF	lung
30	chr3:101076200-101102000	Weak transcription	Lung	lung
31	chr3:101076200-101105600	Weak transcription	Esophagus	oesophagus
32	chr3:101076600-101091400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:101076600-101096400	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:101076800-101092800	Weak transcription	Fetal Muscle Leg	muscle
35	chr3:101076800-101093400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:101077000-101086800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr3:101077000-101095800	Weak transcription	Colon Smooth Muscle	Colon
38	chr3:101077000-101096000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr3:101077000-101102200	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:101077200-101089000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:101077800-101085800	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr3:101077800-101086600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:101077800-101086800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr3:101077800-101094400	Weak transcription	Fetal Intestine Small	intestine
45	chr3:101077800-101096000	Weak transcription	Small Intestine	intestine
46	chr3:101077800-101101000	Weak transcription	NHDF-Ad	bronchial
47	chr3:101077800-101102000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:101078000-101084800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:101078200-101093200	Weak transcription	GM12878-XiMat	blood
50	chr3:101078800-101086000	Strong transcription	Primary T helper cells PMA-I stimulated	--

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