Variant report

Variant	rs924685
Chromosome Location	chr4:78848922-78848923
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10005531	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10018117	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10019920	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10026176	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10027634	0.84[EUR][1000 genomes]
rs10027739	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10030568	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10049674	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1106457	0.92[CEU][hapmap]
rs11931471	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11931686	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11942975	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12509847	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13131331	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13131974	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1393643	0.83[ASN][1000 genomes]
rs1604609	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2036455	0.92[CEU][hapmap]
rs2036457	0.92[CEU][hapmap]
rs2088995	0.83[ASN][1000 genomes]
rs2102192	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28417234	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28436599	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28483318	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28685099	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4128860	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4328941	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4859512	1.00[CEU][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859513	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4859882	0.93[CEU][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4859884	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4859890	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533355	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533372	0.84[CEU][hapmap];0.86[ASN][1000 genomes]
rs67814821	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6814088	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6820725	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6849145	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7436080	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7660788	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7682450	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs873280	0.92[CEU][hapmap]
rs924684	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9985806	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9994366	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	nsv516836	chr4:78748977-78981919	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv594704	chr4:78748977-78981919	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv461562	chr4:78757015-78981919	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv461563	chr4:78757015-78981919	Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv594705	chr4:78757015-78981919	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv1008217	chr4:78777531-78957311	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv537145	chr4:78777531-78957311	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers 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	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs924685	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78784800-78859800	Weak transcription	Esophagus	oesophagus
2	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
3	chr4:78794000-78851200	Weak transcription	Spleen	Spleen
4	chr4:78794200-78851800	Weak transcription	Lung	lung
5	chr4:78802400-78858400	Weak transcription	Aorta	Aorta
6	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:78806600-78875600	Weak transcription	Colonic Mucosa	Colon
8	chr4:78808800-78852400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr4:78809600-78851200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:78809600-78851400	Weak transcription	Ovary	ovary
11	chr4:78809600-78865400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr4:78809600-78881200	Weak transcription	Rectal Smooth Muscle	rectum
13	chr4:78810000-78851800	Weak transcription	Thymus	Thymus
14	chr4:78814600-78874400	Weak transcription	Pancreas	Pancrea
15	chr4:78816400-78866400	Weak transcription	Fetal Thymus	thymus
16	chr4:78816400-78876000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr4:78816600-78851400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr4:78816600-78875800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr4:78818800-78872800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr4:78819200-78852000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr4:78819600-78851200	Weak transcription	Adipose Nuclei	Adipose
22	chr4:78820800-78851200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr4:78821000-78849000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr4:78821000-78866000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr4:78821400-78873200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr4:78830000-78866600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr4:78830200-78851200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr4:78830200-78852000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr4:78830400-78877000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr4:78831800-78865800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr4:78832000-78851400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr4:78832000-78858000	Weak transcription	Fetal Stomach	stomach
33	chr4:78833400-78851400	Weak transcription	Liver	Liver
34	chr4:78833600-78865400	Weak transcription	Fetal Kidney	kidney
35	chr4:78834000-78852800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr4:78835400-78852600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:78838600-78851000	Weak transcription	GM12878-XiMat	blood
38	chr4:78840800-78849200	Weak transcription	Colon Smooth Muscle	Colon
39	chr4:78842200-78865600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:78842400-78865400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:78842800-78851600	Weak transcription	HSMMtube	muscle
42	chr4:78843800-78849000	Weak transcription	NHLF	lung
43	chr4:78843800-78849200	Weak transcription	Fetal Lung	lung
44	chr4:78843800-78851800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr4:78843800-78852800	Weak transcription	Placenta	Placenta
46	chr4:78843800-78854200	Weak transcription	Gastric	stomach
47	chr4:78843800-78858000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:78843800-78858000	Weak transcription	Left Ventricle	heart
49	chr4:78843800-78865200	Weak transcription	Psoas Muscle	Psoas
50	chr4:78844000-78849000	Weak transcription	A549	lung

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