Variant report

Variant	rs6439819
Chromosome Location	chr3:138489798-138489799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:138489312..138491006-chr3:138494503..138496803,2	K562	blood:

Variant related genes	Relation type
ENSG00000239207	Chromatin interaction

Extended variants
information (count: 134 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs1066197	0.87[EUR][1000 genomes]
rs1068104	0.88[EUR][1000 genomes]
rs1068685	0.88[EUR][1000 genomes]
rs11705762	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11709768	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11713049	0.94[EUR][1000 genomes]
rs11717457	0.90[EUR][1000 genomes]
rs11720178	0.88[EUR][1000 genomes]
rs11924814	0.94[EUR][1000 genomes]
rs13069296	0.89[EUR][1000 genomes]
rs13082808	0.93[EUR][1000 genomes]
rs13433948	0.85[EUR][1000 genomes]
rs1400266	0.94[EUR][1000 genomes]
rs1663556	0.89[EUR][1000 genomes]
rs1673597	0.88[EUR][1000 genomes]
rs168633	0.91[EUR][1000 genomes]
rs181729	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs187245	0.81[EUR][1000 genomes]
rs191713	0.92[EUR][1000 genomes]
rs191714	0.93[EUR][1000 genomes]
rs191775	0.93[EUR][1000 genomes]
rs2197387	0.94[EUR][1000 genomes]
rs2348147	0.83[EUR][1000 genomes]
rs244380	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs244381	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2595928	0.86[EUR][1000 genomes]
rs2595930	0.89[EUR][1000 genomes]
rs2607796	0.87[EUR][1000 genomes]
rs28376988	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28408150	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35214574	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs361054	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs361057	0.88[EUR][1000 genomes]
rs361059	0.93[EUR][1000 genomes]
rs361060	0.93[EUR][1000 genomes]
rs361061	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361062	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs361063	0.89[EUR][1000 genomes]
rs361066	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs361067	0.95[EUR][1000 genomes]
rs361068	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs361069	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs361071	0.95[EUR][1000 genomes]
rs361072	0.95[EUR][1000 genomes]
rs361080	0.93[EUR][1000 genomes]
rs361081	0.93[EUR][1000 genomes]
rs361082	0.93[EUR][1000 genomes]
rs361083	0.92[EUR][1000 genomes]
rs361084	0.93[EUR][1000 genomes]
rs361088	0.88[EUR][1000 genomes]
rs361089	0.88[EUR][1000 genomes]
rs361092	0.89[EUR][1000 genomes]
rs361094	0.89[EUR][1000 genomes]
rs361097	0.88[EUR][1000 genomes]
rs371762	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs385254	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs398065	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs404110	0.95[EUR][1000 genomes]
rs409507	0.93[EUR][1000 genomes]
rs413147	0.94[EUR][1000 genomes]
rs425901	0.90[EUR][1000 genomes]
rs4305444	0.93[EUR][1000 genomes]
rs439720	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs448808	0.91[EUR][1000 genomes]
rs470359	0.89[EUR][1000 genomes]
rs473388	0.95[EUR][1000 genomes]
rs475254	0.89[EUR][1000 genomes]
rs476800	0.95[EUR][1000 genomes]
rs482334	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4894350	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4894351	0.94[EUR][1000 genomes]
rs4894352	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4894353	0.93[EUR][1000 genomes]
rs4894354	0.91[EUR][1000 genomes]
rs491371	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs497900	0.93[EUR][1000 genomes]
rs500687	0.95[EUR][1000 genomes]
rs511207	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs524164	0.89[EUR][1000 genomes]
rs539156	0.90[EUR][1000 genomes]
rs539619	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs540198	0.94[EUR][1000 genomes]
rs540907	0.93[EUR][1000 genomes]
rs550768	0.88[EUR][1000 genomes]
rs558905	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs559160	0.89[EUR][1000 genomes]
rs559451	0.91[EUR][1000 genomes]
rs564455	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs589986	0.88[EUR][1000 genomes]
rs603723	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs607044	0.95[EUR][1000 genomes]
rs618457	0.86[EUR][1000 genomes]
rs621204	0.88[EUR][1000 genomes]
rs62282169	0.90[EUR][1000 genomes]
rs624099	0.89[EUR][1000 genomes]
rs625468	0.89[EUR][1000 genomes]
rs635592	0.88[EUR][1000 genomes]
rs6439817	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs647972	0.95[EUR][1000 genomes]
rs654459	0.81[EUR][1000 genomes]
rs6776585	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6781914	0.88[EUR][1000 genomes]
rs6784610	0.82[EUR][1000 genomes]
rs6794270	0.83[EUR][1000 genomes]
rs6795203	0.92[EUR][1000 genomes]
rs6801207	0.94[EUR][1000 genomes]
rs6810351	0.94[EUR][1000 genomes]
rs7612106	0.94[EUR][1000 genomes]
rs7643722	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs772612	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs773045	0.89[EUR][1000 genomes]
rs773184	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9821694	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9822714	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9823213	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9832012	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9834963	0.94[EUR][1000 genomes]
rs9853819	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9863481	0.81[EUR][1000 genomes]
rs9864176	0.89[EUR][1000 genomes]
rs9874723	0.82[EUR][1000 genomes]
rs9877108	0.82[EUR][1000 genomes]
rs9879784	0.89[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
rs6439819	CEP70	Cis_1M	lymphoblastoid	RTeQTL
rs6439819	FAIM	cis	Muscle Skeletal	GTEx
rs6439819	PIK3CB	Cis_1M	lymphoblastoid	RTeQTL

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

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	chr3:138408400-138499200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr3:138460400-138493200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr3:138467600-138492800	Weak transcription	Fetal Heart	heart
6	chr3:138475400-138494200	Weak transcription	Psoas Muscle	Psoas
7	chr3:138476400-138494000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:138482800-138493000	Weak transcription	Right Atrium	heart
9	chr3:138483800-138492800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:138484200-138492600	Weak transcription	HMEC	breast
11	chr3:138484800-138493000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:138485000-138492200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:138486200-138491200	ZNF genes & repeats	K562	blood
14	chr3:138487200-138492800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:138487400-138493000	Weak transcription	Right Ventricle	heart
16	chr3:138487400-138493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr3:138487600-138492600	Weak transcription	Brain Anterior Caudate	brain
18	chr3:138487600-138493000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr3:138487600-138493000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:138487600-138493000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr3:138487600-138494200	Weak transcription	Colonic Mucosa	Colon
22	chr3:138487600-138494200	Weak transcription	Ovary	ovary
23	chr3:138487800-138492800	Weak transcription	Brain Hippocampus Middle	brain
24	chr3:138487800-138493200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:138487800-138493200	Weak transcription	Left Ventricle	heart
26	chr3:138487800-138493400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr3:138488000-138492600	Weak transcription	Brain Substantia Nigra	brain
28	chr3:138488000-138492600	Weak transcription	Fetal Muscle Leg	muscle
29	chr3:138488000-138492600	Weak transcription	NHEK	skin
30	chr3:138488000-138492600	Weak transcription	NHLF	lung
31	chr3:138488000-138493000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:138488000-138493000	Weak transcription	Adipose Nuclei	Adipose
33	chr3:138488000-138493000	Weak transcription	Fetal Brain Female	brain
34	chr3:138488000-138493400	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:138488000-138493400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr3:138488000-138493800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:138488000-138493800	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr3:138488000-138494000	Weak transcription	Pancreas	Pancrea
39	chr3:138488000-138494200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr3:138488000-138494200	Weak transcription	Esophagus	oesophagus
41	chr3:138488000-138494200	Weak transcription	Lung	lung
42	chr3:138488000-138497000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr3:138488000-138497200	Weak transcription	Gastric	stomach
44	chr3:138488000-138498600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:138488000-138499800	Weak transcription	Thymus	Thymus
46	chr3:138488000-138504600	Weak transcription	Primary B cells from cord blood	blood
47	chr3:138488000-138519200	Weak transcription	Spleen	Spleen
48	chr3:138488200-138491200	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr3:138488200-138491600	Weak transcription	Fetal Intestine Small	intestine
50	chr3:138488200-138492000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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