Variant report

Variant	rs3849580
Chromosome Location	chr4:78743877-78743878
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:78738764..78744926-chr4:78780904..78785516,9	MCF-7	breast:
2	chr4:78738995..78744410-chr4:78782336..78785612,12	K562	blood:
3	chr4:78664695..78666373-chr4:78741463..78744231,2	K562	blood:
4	chr4:78741277..78744126-chr4:78747638..78749332,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169288	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11730329	0.86[ASN][1000 genomes]
rs11730403	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11733759	0.85[ASN][1000 genomes]
rs11939576	0.86[ASN][1000 genomes]
rs13131896	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1402626	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1521419	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1554457	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17002823	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17002824	0.86[ASN][1000 genomes]
rs17002825	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17002828	0.86[ASN][1000 genomes]
rs17002829	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17002831	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1813725	0.81[AFR][1000 genomes]
rs1814033	0.80[AFR][1000 genomes]
rs1980266	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2866688	0.86[ASN][1000 genomes]
rs4078523	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4304001	0.86[ASN][1000 genomes]
rs4365752	0.86[ASN][1000 genomes]
rs4410552	0.86[ASN][1000 genomes]
rs55694923	0.86[ASN][1000 genomes]
rs55886549	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs57246363	0.86[ASN][1000 genomes]
rs58218398	0.82[ASN][1000 genomes]
rs58358199	0.80[ASN][1000 genomes]
rs60135456	0.84[ASN][1000 genomes]
rs6533290	0.86[ASN][1000 genomes]
rs6817305	0.86[ASN][1000 genomes]
rs6822317	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6827822	0.84[ASN][1000 genomes]
rs72868269	0.86[ASN][1000 genomes]
rs73827437	0.85[ASN][1000 genomes]
rs73827443	0.86[ASN][1000 genomes]
rs7657658	0.86[ASN][1000 genomes]
rs9996218	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1010714	chr4:78742505-78991030	Weak transcription Genic enhancers Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3849580	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78742200-78744000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
2	chr4:78742400-78744000	Enhancers	Fetal Muscle Leg	muscle
3	chr4:78742400-78744400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr4:78742800-78744600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:78742800-78744600	Enhancers	Duodenum Mucosa	Duodenum
6	chr4:78742800-78744600	Enhancers	Fetal Thymus	thymus
7	chr4:78742800-78744800	Enhancers	Primary B cells from peripheral blood	blood
8	chr4:78742800-78745000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr4:78742800-78745000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr4:78742800-78747200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:78743000-78745400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr4:78743200-78744800	Enhancers	Primary B cells from cord blood	blood
13	chr4:78743200-78745000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr4:78743200-78750000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr4:78743400-78744200	Enhancers	Primary hematopoietic stem cells	blood
16	chr4:78743400-78744400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr4:78743400-78744600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr4:78743400-78744600	Enhancers	Thymus	Thymus
19	chr4:78743400-78745600	Enhancers	Primary T cells from cord blood	blood
20	chr4:78743400-78745600	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr4:78743400-78749800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr4:78743400-78750200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:78743600-78744200	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr4:78743800-78744000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr4:78743800-78744600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr4:78743800-78745000	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr4:78743800-78747800	Weak transcription	Dnd41	blood
28	chr4:78743800-78748200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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