Variant report

Variant	rs772612
Chromosome Location	chr3:138472335-138472336
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:138464471..138467616-chr3:138469516..138472812,3	K562	blood:
2	chr3:138471278..138473423-chr3:138476581..138478360,2	K562	blood:
3	chr3:138464449..138466170-chr3:138471312..138473227,2	K562	blood:

Variant related genes	Relation type
ENSG00000051382	Chromatin interaction

Extended variants
information (count: 141 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1066197	0.89[EUR][1000 genomes]
rs1068104	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1068685	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11705762	0.96[EUR][1000 genomes]
rs11709768	0.97[EUR][1000 genomes]
rs11713049	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11717457	0.90[EUR][1000 genomes]
rs11720178	0.90[EUR][1000 genomes]
rs11924814	0.97[EUR][1000 genomes]
rs13069296	0.91[EUR][1000 genomes]
rs13082808	0.96[EUR][1000 genomes]
rs13433948	0.87[EUR][1000 genomes]
rs1400266	0.97[EUR][1000 genomes]
rs1663556	0.91[EUR][1000 genomes]
rs1673597	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs168633	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs181729	0.91[EUR][1000 genomes]
rs187245	0.83[EUR][1000 genomes]
rs191713	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs191714	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs191775	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2197387	0.98[EUR][1000 genomes]
rs2348147	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs244380	0.96[EUR][1000 genomes]
rs244381	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2595928	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2595930	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2607796	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28376988	0.96[EUR][1000 genomes]
rs28408150	0.96[EUR][1000 genomes]
rs2881900	0.80[EUR][1000 genomes]
rs34354181	0.81[EUR][1000 genomes]
rs34900559	0.82[EUR][1000 genomes]
rs35214574	0.93[EUR][1000 genomes]
rs361054	0.97[EUR][1000 genomes]
rs361056	0.88[AFR][1000 genomes]
rs361057	0.90[EUR][1000 genomes]
rs361059	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs361060	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs361061	0.96[EUR][1000 genomes]
rs361062	0.96[EUR][1000 genomes]
rs361063	0.92[EUR][1000 genomes]
rs361064	0.86[AFR][1000 genomes]
rs361066	0.98[EUR][1000 genomes]
rs361067	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs361068	0.98[EUR][1000 genomes]
rs361069	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs361071	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs361072	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs361079	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs361080	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs361081	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs361082	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs361083	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs361084	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs361088	0.91[EUR][1000 genomes]
rs361089	0.90[EUR][1000 genomes]
rs361092	0.91[EUR][1000 genomes]
rs361094	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs361097	0.91[EUR][1000 genomes]
rs371762	0.96[EUR][1000 genomes]
rs385254	0.96[EUR][1000 genomes]
rs398065	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs404110	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs409507	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs413147	0.97[EUR][1000 genomes]
rs425901	0.94[EUR][1000 genomes]
rs4305444	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs439720	0.95[EUR][1000 genomes]
rs448808	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs470359	0.91[EUR][1000 genomes]
rs473388	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs475254	0.91[EUR][1000 genomes]
rs476800	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs482334	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4894350	0.98[EUR][1000 genomes]
rs4894351	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4894352	0.98[EUR][1000 genomes]
rs4894353	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4894354	0.93[EUR][1000 genomes]
rs491371	0.97[EUR][1000 genomes]
rs497900	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs500687	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs511207	0.97[EUR][1000 genomes]
rs524164	0.91[EUR][1000 genomes]
rs539156	0.91[EUR][1000 genomes]
rs539619	0.98[EUR][1000 genomes]
rs540198	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs540907	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs550768	0.90[EUR][1000 genomes]
rs558905	0.98[EUR][1000 genomes]
rs559160	0.91[EUR][1000 genomes]
rs559451	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs564455	0.98[EUR][1000 genomes]
rs589986	0.90[EUR][1000 genomes]
rs603723	0.91[EUR][1000 genomes]
rs607044	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs618457	0.88[EUR][1000 genomes]
rs621204	0.90[EUR][1000 genomes]
rs62282169	0.90[EUR][1000 genomes]
rs624099	0.91[EUR][1000 genomes]
rs625468	0.91[EUR][1000 genomes]
rs635592	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6439817	0.96[EUR][1000 genomes]
rs6439819	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs647972	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs654459	0.83[EUR][1000 genomes]
rs6776585	0.96[EUR][1000 genomes]
rs6781914	0.88[EUR][1000 genomes]
rs6784610	0.83[EUR][1000 genomes]
rs6794270	0.84[EUR][1000 genomes]
rs6795203	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6801207	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6810351	0.96[EUR][1000 genomes]
rs7612106	0.96[EUR][1000 genomes]
rs7643722	0.96[EUR][1000 genomes]
rs773045	0.91[EUR][1000 genomes]
rs773184	0.90[EUR][1000 genomes]
rs9818354	0.81[EUR][1000 genomes]
rs9821694	0.98[EUR][1000 genomes]
rs9822714	0.98[EUR][1000 genomes]
rs9823213	0.95[EUR][1000 genomes]
rs9832012	0.97[EUR][1000 genomes]
rs9834963	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9853819	0.94[EUR][1000 genomes]
rs9863481	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9864176	0.91[EUR][1000 genomes]
rs9874723	0.84[EUR][1000 genomes]
rs9877108	0.83[EUR][1000 genomes]
rs9879784	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	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
5	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
6	nsv869205	chr3:138248190-138775288	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv868955	chr3:138248190-138848947	Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats 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	37 gene(s)	inside rSNPs	diseases
8	nsv591854	chr3:138348081-138764229	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1010514	chr3:138365640-138737688	Flanking Bivalent TSS/Enh Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv1000927	chr3:138423543-138632596	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv917964	chr3:138440701-138699084	Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs772612	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs772612	FAIM	cis	Muscle Skeletal	GTEx
rs772612	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138369000-138493000	Weak transcription	Fetal Lung	lung
2	chr3:138393800-138515000	Weak transcription	Aorta	Aorta
3	chr3:138395800-138480200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr3:138396200-138486400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:138396200-138487000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:138408000-138479800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:138408400-138499200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:138413800-138487600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:138416800-138486600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:138417800-138486600	Weak transcription	Hela-S3	cervix
11	chr3:138419000-138487000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:138419200-138486200	Weak transcription	Fetal Muscle Leg	muscle
13	chr3:138421800-138479800	Weak transcription	Small Intestine	intestine
14	chr3:138423400-138487000	Weak transcription	Colonic Mucosa	Colon
15	chr3:138438600-138486400	Weak transcription	Esophagus	oesophagus
16	chr3:138443000-138483200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:138443800-138474400	Weak transcription	Brain Angular Gyrus	brain
18	chr3:138445000-138478000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:138446000-138486200	Weak transcription	GM12878-XiMat	blood
20	chr3:138446200-138483600	Weak transcription	NH-A	brain
21	chr3:138452400-138473400	Weak transcription	Primary B cells from peripheral blood	blood
22	chr3:138454400-138486400	Weak transcription	HSMM	muscle
23	chr3:138455200-138486400	Weak transcription	Spleen	Spleen
24	chr3:138459800-138482800	Weak transcription	Lung	lung
25	chr3:138459800-138483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:138460200-138486400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr3:138460200-138486400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:138460400-138473400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:138460400-138483400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:138460400-138486200	Weak transcription	Brain Hippocampus Middle	brain
31	chr3:138460400-138486200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr3:138460400-138486600	Weak transcription	Ovary	ovary
33	chr3:138460400-138486800	Weak transcription	Brain Anterior Caudate	brain
34	chr3:138460400-138493200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr3:138460600-138483200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:138460600-138486200	Weak transcription	Adipose Nuclei	Adipose
37	chr3:138460600-138486200	Weak transcription	Thymus	Thymus
38	chr3:138460600-138486400	Weak transcription	Gastric	stomach
39	chr3:138460600-138486600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:138460600-138487000	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr3:138460600-138487200	Weak transcription	Left Ventricle	heart
42	chr3:138461000-138473800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:138461000-138479000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:138461200-138480000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:138461200-138483400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:138461600-138472400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr3:138461600-138473000	Weak transcription	Liver	Liver
48	chr3:138461600-138474000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:138462800-138482400	Weak transcription	Osteobl	bone
50	chr3:138462800-138486200	Weak transcription	Fetal Stomach	stomach

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