Variant report

Variant	rs6762114
Chromosome Location	chr3:138239898-138239899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1082034	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1082037	0.84[EUR][1000 genomes]
rs1088055	0.87[EUR][1000 genomes]
rs10935287	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11709290	0.81[ASN][1000 genomes]
rs11717771	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12487652	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12487694	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12490633	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12497070	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12636246	0.83[ASN][1000 genomes]
rs12636910	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13098789	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13101081	0.87[EUR][1000 genomes]
rs1379257	0.83[EUR][1000 genomes]
rs1479930	0.83[EUR][1000 genomes]
rs1600511	0.83[EUR][1000 genomes]
rs1625751	0.92[ASN][1000 genomes]
rs1672927	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1672928	0.81[AMR][1000 genomes]
rs1672931	0.81[AMR][1000 genomes]
rs1672932	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1672933	0.81[AMR][1000 genomes]
rs1672936	0.80[AMR][1000 genomes]
rs1672938	0.82[EUR][1000 genomes]
rs1672939	0.80[EUR][1000 genomes]
rs1672963	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1673593	0.83[EUR][1000 genomes]
rs1673594	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1673607	0.82[EUR][1000 genomes]
rs1673608	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1673622	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1679165	0.82[ASN][1000 genomes]
rs1679169	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1720833	0.92[ASN][1000 genomes]
rs2086351	0.92[ASN][1000 genomes]
rs2607790	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28719641	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2881793	0.89[EUR][1000 genomes]
rs35471402	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35500947	0.96[ASN][1000 genomes]
rs35549884	0.80[ASN][1000 genomes]
rs35932955	0.90[ASN][1000 genomes]
rs3813264	0.82[ASN][1000 genomes]
rs3884240	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4432674	0.83[EUR][1000 genomes]
rs4678264	0.83[EUR][1000 genomes]
rs4678266	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4894389	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs497334	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs503922	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs529615	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs537210	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs542010	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550507	0.86[EUR][1000 genomes]
rs56394118	0.96[ASN][1000 genomes]
rs564800	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs582386	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60513493	0.80[EUR][1000 genomes]
rs609797	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs611134	0.87[EUR][1000 genomes]
rs612471	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61258082	0.80[ASN][1000 genomes]
rs618792	0.81[EUR][1000 genomes]
rs620035	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs629884	0.87[EUR][1000 genomes]
rs6439809	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6439810	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs654528	0.81[AMR][1000 genomes]
rs656107	0.90[ASN][1000 genomes]
rs6771237	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs680070	0.83[EUR][1000 genomes]
rs73229526	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7625326	0.87[EUR][1000 genomes]
rs7626226	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7627685	0.85[EUR][1000 genomes]
rs7634745	0.85[EUR][1000 genomes]
rs7643973	0.87[EUR][1000 genomes]
rs7645920	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7653815	0.85[EUR][1000 genomes]
rs773443	0.92[ASN][1000 genomes]
rs773444	0.81[EUR][1000 genomes]
rs773445	0.84[EUR][1000 genomes]
rs773450	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs773455	0.82[AMR][1000 genomes]
rs774011	0.92[ASN][1000 genomes]
rs774012	0.92[ASN][1000 genomes]
rs811793	0.83[EUR][1000 genomes]
rs814022	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs936316	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9681127	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9811052	0.87[EUR][1000 genomes]
rs9817419	0.87[EUR][1000 genomes]
rs9822037	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9823182	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9827256	0.87[EUR][1000 genomes]
rs9848718	0.87[EUR][1000 genomes]
rs9848938	0.81[ASN][1000 genomes]
rs9853998	0.86[EUR][1000 genomes]
rs9855306	0.92[ASN][1000 genomes]
rs9878436	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv877538	chr3:138218709-138311201	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv1009726	chr3:138219923-138737688	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv877539	chr3:138224220-138261288	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6762114	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs6762114	FAIM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138194000-138260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:138209800-138258600	Weak transcription	Primary T cells from cord blood	blood
3	chr3:138210400-138242000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:138210800-138260600	Weak transcription	Colonic Mucosa	Colon
5	chr3:138211200-138260600	Weak transcription	Brain Angular Gyrus	brain
6	chr3:138211800-138260600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:138212600-138250200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:138212800-138249800	Weak transcription	Small Intestine	intestine
9	chr3:138213200-138243800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr3:138214400-138260600	Weak transcription	Right Ventricle	heart
11	chr3:138218600-138254000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:138219000-138247000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr3:138219400-138263200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:138225400-138259600	Weak transcription	Brain Anterior Caudate	brain
15	chr3:138231200-138260600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:138232000-138258200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:138232000-138260600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:138232200-138242000	Weak transcription	Psoas Muscle	Psoas
19	chr3:138232200-138260600	Weak transcription	Left Ventricle	heart
20	chr3:138232200-138260600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:138232400-138249600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:138233800-138243000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:138235600-138260600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:138236000-138260000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr3:138236000-138264800	Weak transcription	Fetal Heart	heart
26	chr3:138236200-138260000	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:138237200-138244400	Weak transcription	Dnd41	blood
28	chr3:138237200-138246200	Weak transcription	Brain Hippocampus Middle	brain
29	chr3:138237200-138247000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:138237200-138247000	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr3:138237200-138249600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:138237200-138260400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr3:138237400-138240800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr3:138237400-138242200	Weak transcription	Gastric	stomach
35	chr3:138237400-138244400	Weak transcription	Liver	Liver
36	chr3:138237400-138245000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:138237400-138245000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr3:138237400-138246000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr3:138237400-138246800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:138237400-138248600	Weak transcription	Adipose Nuclei	Adipose
41	chr3:138237400-138252400	Weak transcription	Fetal Lung	lung
42	chr3:138237400-138252400	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:138237400-138254400	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:138237400-138258400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:138237400-138260400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:138237400-138260600	Weak transcription	Aorta	Aorta
47	chr3:138237600-138260600	Weak transcription	Brain Substantia Nigra	brain
48	chr3:138239000-138240400	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:138239000-138241000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:138239200-138241000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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