Variant report

Variant	rs7698009
Chromosome Location	chr4:78721502-78721503
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78717746..78719654-chr4:78721181..78723626,2	K562	blood:
2	chr4:78718708..78721606-chr4:78722272..78724950,3	K562	blood:
3	chr4:78720260..78722525-chr4:78782700..78784492,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169288	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10005935	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1587563	0.85[ASN][1000 genomes]
rs17002804	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6533225	0.80[AFR][1000 genomes]
rs6811439	0.84[ASN][1000 genomes]
rs6816134	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6825492	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6835993	0.82[AFR][1000 genomes]
rs9654194	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829976	chr4:78576657-78757798	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv879501	chr4:78647634-78866007	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	esv1818157	chr4:78678104-78849088	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2752050	chr4:78693311-78975321	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7698009	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78694200-78722000	Weak transcription	Fetal Stomach	stomach
2	chr4:78704800-78722200	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr4:78710200-78722000	Enhancers	Primary T killer memory cells from peripheral blood	blood
4	chr4:78711000-78722200	Weak transcription	Ovary	ovary
5	chr4:78711400-78722000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr4:78711600-78722200	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:78711800-78721800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr4:78712800-78722000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr4:78713600-78721600	Weak transcription	HUVEC	blood vessel
10	chr4:78714200-78721600	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:78716400-78722000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:78716400-78733400	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:78716600-78722000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr4:78716800-78721800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:78717600-78722200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:78718000-78721800	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:78718200-78721600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr4:78718200-78721800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr4:78718200-78728200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr4:78718800-78721800	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:78718800-78721800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:78718800-78738600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr4:78719000-78721800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr4:78719000-78721800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:78719000-78721800	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr4:78719000-78722000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr4:78719000-78722000	Weak transcription	NHEK	skin
28	chr4:78719200-78721800	Weak transcription	A549	lung
29	chr4:78719200-78721800	Weak transcription	HMEC	breast
30	chr4:78719200-78722000	Weak transcription	HSMM	muscle
31	chr4:78719200-78722200	Enhancers	Primary T cells fromperipheralblood	blood
32	chr4:78719200-78723200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr4:78719400-78721600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:78719400-78722200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr4:78720000-78723400	Enhancers	Psoas Muscle	Psoas
36	chr4:78720200-78721600	Enhancers	Esophagus	oesophagus
37	chr4:78720200-78721800	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr4:78720200-78721800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr4:78720200-78721800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr4:78720200-78722200	Weak transcription	Fetal Thymus	thymus
41	chr4:78720200-78722400	Weak transcription	GM12878-XiMat	blood
42	chr4:78720200-78723000	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr4:78720200-78723200	Enhancers	Left Ventricle	heart
44	chr4:78720400-78722000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr4:78720400-78722000	Weak transcription	Brain Anterior Caudate	brain
46	chr4:78720400-78722000	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr4:78720400-78724000	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr4:78720600-78721800	Weak transcription	Liver	Liver
49	chr4:78720600-78721800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr4:78720600-78722000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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