Variant report

Variant	rs28796999
Chromosome Location	chr4:78810350-78810351
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	chr4:78807806..78810602-chr4:78831657..78833693,2	MCF-7	breast:

Extended variants
information (count: 120 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10005741	0.88[AMR][1000 genomes]
rs1039467	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11097935	0.90[AMR][1000 genomes]
rs11097965	0.87[ASN][1000 genomes]
rs11721383	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11723221	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11727993	0.90[AMR][1000 genomes]
rs11729703	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11730329	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11730403	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11731374	0.98[ASN][1000 genomes]
rs11732039	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11733759	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11734428	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11737353	0.98[ASN][1000 genomes]
rs11939576	0.88[ASN][1000 genomes]
rs13111592	0.88[AMR][1000 genomes]
rs13131896	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13138341	0.84[AMR][1000 genomes]
rs13144225	0.90[AMR][1000 genomes]
rs1402626	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1501373	0.90[AMR][1000 genomes]
rs1521419	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1553386	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1554457	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17002823	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17002824	0.88[ASN][1000 genomes]
rs17002825	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17002828	0.88[ASN][1000 genomes]
rs17002829	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17002831	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1814033	0.90[AMR][1000 genomes]
rs1847216	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1980266	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2134459	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2866688	0.88[ASN][1000 genomes]
rs2866689	0.87[AMR][1000 genomes]
rs28891692	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2903291	0.90[AMR][1000 genomes]
rs4078523	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4304001	0.88[ASN][1000 genomes]
rs4331798	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4365752	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4388114	0.96[ASN][1000 genomes]
rs4410552	0.88[ASN][1000 genomes]
rs4417999	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4473672	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4546268	0.82[ASN][1000 genomes]
rs4607246	0.96[ASN][1000 genomes]
rs4859506	0.90[AMR][1000 genomes]
rs4859871	0.84[AMR][1000 genomes]
rs4859876	0.90[AMR][1000 genomes]
rs4859878	0.90[AMR][1000 genomes]
rs55673370	0.98[ASN][1000 genomes]
rs55694923	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55886549	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56138517	0.82[ASN][1000 genomes]
rs57221952	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57246363	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57501818	1.00[ASN][1000 genomes]
rs57868780	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58054752	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58218398	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58358199	0.94[ASN][1000 genomes]
rs60135456	0.90[ASN][1000 genomes]
rs6533239	0.88[AMR][1000 genomes]
rs6533270	0.90[AMR][1000 genomes]
rs6533272	0.90[AMR][1000 genomes]
rs6533290	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6533358	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6533359	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6817305	0.88[ASN][1000 genomes]
rs6822317	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6827822	0.90[ASN][1000 genomes]
rs6830993	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6832015	0.82[ASN][1000 genomes]
rs6836627	1.00[ASN][1000 genomes]
rs6838630	1.00[ASN][1000 genomes]
rs6850049	0.90[AMR][1000 genomes]
rs6850590	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6854989	0.82[ASN][1000 genomes]
rs6855336	0.90[AMR][1000 genomes]
rs6857067	0.90[AMR][1000 genomes]
rs72868269	0.88[ASN][1000 genomes]
rs72869573	0.83[ASN][1000 genomes]
rs73827437	0.87[ASN][1000 genomes]
rs73827443	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73827451	0.96[ASN][1000 genomes]
rs73827456	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73827459	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73827460	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7655949	0.90[AMR][1000 genomes]
rs7657658	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7661064	1.00[ASN][1000 genomes]
rs7663359	0.82[ASN][1000 genomes]
rs7669988	0.90[AMR][1000 genomes]
rs7671941	0.83[ASN][1000 genomes]
rs7675586	0.97[ASN][1000 genomes]
rs7687170	0.82[ASN][1000 genomes]
rs7687812	1.00[ASN][1000 genomes]
rs7689226	0.97[ASN][1000 genomes]
rs7692075	0.99[ASN][1000 genomes]
rs7693256	0.82[AMR][1000 genomes]
rs885376	0.84[AMR][1000 genomes]
rs9991424	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9993942	0.90[AMR][1000 genomes]
rs9996218	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv1824966	chr4:78747771-78823070	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
rs28796999	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78784800-78842200	Weak transcription	HSMMtube	muscle
2	chr4:78784800-78859800	Weak transcription	Esophagus	oesophagus
3	chr4:78785000-78810600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:78785000-78831200	Weak transcription	Brain Angular Gyrus	brain
5	chr4:78785000-78831600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:78785000-78841800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:78785000-78874400	Weak transcription	Right Ventricle	heart
8	chr4:78785200-78816200	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:78785200-78818800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr4:78785200-78820800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr4:78785400-78829800	Weak transcription	Fetal Heart	heart
12	chr4:78790600-78843400	Weak transcription	Small Intestine	intestine
13	chr4:78790800-78817400	Weak transcription	NH-A	brain
14	chr4:78794000-78851200	Weak transcription	Spleen	Spleen
15	chr4:78794200-78815600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:78794200-78851800	Weak transcription	Lung	lung
17	chr4:78795600-78814600	Weak transcription	HSMM	muscle
18	chr4:78795600-78831800	Weak transcription	NHLF	lung
19	chr4:78795600-78833000	Weak transcription	Brain Germinal Matrix	brain
20	chr4:78799200-78832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:78802200-78811000	Weak transcription	Psoas Muscle	Psoas
22	chr4:78802400-78814200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:78802400-78858400	Weak transcription	Aorta	Aorta
24	chr4:78802800-78810400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr4:78802800-78810600	Weak transcription	Gastric	stomach
26	chr4:78803400-78814600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr4:78803400-78817600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr4:78803600-78810600	Strong transcription	Adipose Nuclei	Adipose
29	chr4:78803800-78810600	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr4:78804000-78810600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr4:78804400-78810400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr4:78804600-78810400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:78804800-78810400	Strong transcription	Fetal Muscle Leg	muscle
34	chr4:78805200-78810400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:78806000-78813600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr4:78806000-78817600	Weak transcription	HMEC	breast
37	chr4:78806000-78817800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:78806000-78841400	Weak transcription	A549	lung
39	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
40	chr4:78806600-78875600	Weak transcription	Colonic Mucosa	Colon
41	chr4:78807200-78813600	Weak transcription	NHDF-Ad	bronchial
42	chr4:78807400-78818200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr4:78808800-78814400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr4:78808800-78819000	Weak transcription	NHEK	skin
45	chr4:78808800-78820600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr4:78808800-78852400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr4:78809000-78811600	Weak transcription	Colon Smooth Muscle	Colon
48	chr4:78809000-78812400	Weak transcription	Osteobl	bone
49	chr4:78809000-78813800	Weak transcription	Pancreas	Pancrea
50	chr4:78809000-78817400	Weak transcription	K562	blood

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