Variant report

Variant	rs12496260
Chromosome Location	chr3:101221703-101221704
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1019677	0.93[EUR][1000 genomes]
rs10936607	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10936642	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10936664	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12491955	0.89[EUR][1000 genomes]
rs13062095	0.80[EUR][1000 genomes]
rs13087404	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13088318	0.85[EUR][1000 genomes]
rs13320918	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13322987	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs16843927	0.82[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs1918405	0.93[EUR][1000 genomes]
rs2141179	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141180	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2178036	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2250611	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2317699	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2317700	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2317745	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2317749	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2317751	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2433031	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2553416	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2553424	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2553427	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2553430	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2682383	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2682384	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2682386	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2682390	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2682391	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28460520	0.84[EUR][1000 genomes]
rs28565548	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34255148	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3846091	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4287896	0.93[EUR][1000 genomes]
rs4683899	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683900	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4683917	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683918	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs473702	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs497953	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs508537	0.82[EUR][1000 genomes]
rs520558	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs551442	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56075912	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62280667	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441602	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6441608	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6441610	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6771561	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6772703	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs6773536	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7628681	0.93[EUR][1000 genomes]
rs7631506	0.82[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs7636475	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9814991	0.95[EUR][1000 genomes]
rs9843186	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9856435	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9859077	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9874188	0.87[EUR][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	esv1803745	chr3:101196030-101230330	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12496260	SENP7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101171200-101230400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:101186400-101223600	Weak transcription	Gastric	stomach
3	chr3:101193200-101230400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:101198600-101231000	Weak transcription	GM12878-XiMat	blood
5	chr3:101202200-101230800	Weak transcription	Psoas Muscle	Psoas
6	chr3:101204000-101231200	Weak transcription	Esophagus	oesophagus
7	chr3:101204200-101223800	Weak transcription	NH-A	brain
8	chr3:101204200-101227600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:101204200-101228400	Weak transcription	NHDF-Ad	bronchial
10	chr3:101204400-101225600	Weak transcription	K562	blood
11	chr3:101204400-101230800	Weak transcription	Right Ventricle	heart
12	chr3:101204600-101230800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr3:101206800-101224800	Weak transcription	Fetal Heart	heart
14	chr3:101207200-101221800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:101207800-101231000	Weak transcription	Aorta	Aorta
16	chr3:101209600-101227800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr3:101210000-101231200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:101211200-101231000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:101211600-101230400	Weak transcription	Placenta	Placenta
20	chr3:101211800-101221800	Weak transcription	HepG2	liver
21	chr3:101211800-101223600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:101211800-101227400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:101211800-101228200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr3:101211800-101229600	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:101211800-101230400	Weak transcription	Liver	Liver
26	chr3:101211800-101230800	Weak transcription	Lung	lung
27	chr3:101211800-101231400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:101212000-101229400	Weak transcription	Fetal Brain Male	brain
29	chr3:101212000-101230000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:101212000-101230200	Weak transcription	Adipose Nuclei	Adipose
31	chr3:101212200-101223200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:101212200-101223600	Weak transcription	Fetal Intestine Large	intestine
33	chr3:101212200-101228200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:101212200-101229800	Weak transcription	Brain Cingulate Gyrus	brain
35	chr3:101212200-101230000	Weak transcription	Colon Smooth Muscle	Colon
36	chr3:101212200-101230000	Weak transcription	Fetal Brain Female	brain
37	chr3:101212200-101230200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr3:101212200-101230200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr3:101212200-101230600	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:101212200-101230800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:101212200-101230800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:101212200-101230800	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:101212200-101230800	Weak transcription	Fetal Kidney	kidney
44	chr3:101212200-101230800	Weak transcription	Left Ventricle	heart
45	chr3:101212200-101230800	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:101212200-101230800	Weak transcription	HSMM	muscle
47	chr3:101212200-101231000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:101212200-101231000	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr3:101212200-101231000	Weak transcription	Spleen	Spleen
50	chr3:101212400-101222200	Weak transcription	Brain Anterior Caudate	brain

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