Variant report

Variant	rs9991424
Chromosome Location	chr4:78878846-78878847
allele	A/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:78739575..78741919-chr4:78878334..78880056,2	MCF-7	breast:
2	chr4:78876905..78879024-chr4:78879290..78880941,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248926	Chromatin interaction
ENSG00000138767	Chromatin interaction

Extended variants
information (count: 129 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10005741	0.88[AMR][1000 genomes]
rs1010728	0.88[ASN][1000 genomes]
rs1039467	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10428319	0.88[ASN][1000 genomes]
rs10856991	0.97[ASN][1000 genomes]
rs11097935	0.91[AMR][1000 genomes]
rs11097965	0.83[ASN][1000 genomes]
rs11097980	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11721383	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11723221	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11727993	0.91[AMR][1000 genomes]
rs11729703	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11730329	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11730403	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11732039	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11733759	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11734428	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11937191	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12108312	0.90[ASN][1000 genomes]
rs12507708	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12650649	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13111592	0.88[AMR][1000 genomes]
rs13131896	0.91[AMR][1000 genomes]
rs13144225	0.91[AMR][1000 genomes]
rs1402626	0.85[AMR][1000 genomes]
rs1501373	0.91[AMR][1000 genomes]
rs1502879	0.91[ASN][1000 genomes]
rs1502880	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1521419	0.91[AMR][1000 genomes]
rs1553386	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1554457	0.91[AMR][1000 genomes]
rs17002823	0.91[AMR][1000 genomes]
rs17002825	0.91[AMR][1000 genomes]
rs17002829	0.85[AMR][1000 genomes]
rs17002831	0.85[AMR][1000 genomes]
rs1814033	0.91[AMR][1000 genomes]
rs1847215	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1847216	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1910304	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1980266	0.91[AMR][1000 genomes]
rs2036458	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2102190	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2134459	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2174078	0.95[ASN][1000 genomes]
rs2174079	0.89[ASN][1000 genomes]
rs2174080	0.88[ASN][1000 genomes]
rs28796999	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28891692	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2903291	0.91[AMR][1000 genomes]
rs35896758	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3860617	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4078523	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4331798	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4365752	0.91[AMR][1000 genomes]
rs4417999	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4473672	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4546268	0.88[ASN][1000 genomes]
rs4561950	0.88[ASN][1000 genomes]
rs4859506	0.91[AMR][1000 genomes]
rs4859515	0.87[ASN][1000 genomes]
rs4859876	0.91[AMR][1000 genomes]
rs4859878	0.91[AMR][1000 genomes]
rs4859894	0.87[ASN][1000 genomes]
rs4859896	0.87[ASN][1000 genomes]
rs4859897	0.87[ASN][1000 genomes]
rs4859898	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4859899	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859900	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859901	0.89[ASN][1000 genomes]
rs55694923	0.85[AMR][1000 genomes]
rs55886549	0.91[AMR][1000 genomes]
rs56138517	0.88[ASN][1000 genomes]
rs57221952	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57246363	0.91[AMR][1000 genomes]
rs57868780	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57896992	0.88[ASN][1000 genomes]
rs58054752	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58218398	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6533239	0.88[AMR][1000 genomes]
rs6533270	0.91[AMR][1000 genomes]
rs6533272	0.91[AMR][1000 genomes]
rs6533290	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6533358	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533359	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6533374	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6533376	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6533382	0.89[ASN][1000 genomes]
rs6821826	0.88[ASN][1000 genomes]
rs6822317	0.91[AMR][1000 genomes]
rs6830993	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6832015	0.88[ASN][1000 genomes]
rs6850049	0.91[AMR][1000 genomes]
rs6850590	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6851286	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6854989	0.88[ASN][1000 genomes]
rs6855336	0.91[AMR][1000 genomes]
rs6857067	0.91[AMR][1000 genomes]
rs6857479	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72869573	0.87[ASN][1000 genomes]
rs73827443	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73827456	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73827459	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73827460	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7439347	0.88[ASN][1000 genomes]
rs7655949	0.91[AMR][1000 genomes]
rs7656319	0.90[ASN][1000 genomes]
rs7657658	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7659122	0.90[ASN][1000 genomes]
rs7663359	0.88[ASN][1000 genomes]
rs7669988	0.91[AMR][1000 genomes]
rs7671432	0.87[ASN][1000 genomes]
rs7671941	0.87[ASN][1000 genomes]
rs7673642	0.90[ASN][1000 genomes]
rs7687170	0.88[ASN][1000 genomes]
rs7693256	0.82[AMR][1000 genomes]
rs7699987	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs950263	0.87[ASN][1000 genomes]
rs950264	0.87[ASN][1000 genomes]
rs9993942	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
rs9991424	CNOT6L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78806000-78881000	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:78809600-78881200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:78849600-78881000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:78850200-78881000	Weak transcription	A549	lung
5	chr4:78852000-78881200	Weak transcription	Lung	lung
6	chr4:78853200-78880800	Weak transcription	Osteobl	bone
7	chr4:78853200-78881000	Weak transcription	Brain Anterior Caudate	brain
8	chr4:78859400-78879000	Weak transcription	Small Intestine	intestine
9	chr4:78863400-78880800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:78865800-78881000	Weak transcription	Psoas Muscle	Psoas
11	chr4:78866800-78881000	Weak transcription	Fetal Kidney	kidney
12	chr4:78868600-78881000	Weak transcription	Brain Angular Gyrus	brain
13	chr4:78869000-78879600	Weak transcription	Spleen	Spleen
14	chr4:78870400-78881000	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:78872400-78880800	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr4:78872600-78880800	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:78873400-78881200	Weak transcription	Left Ventricle	heart
18	chr4:78874200-78881000	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr4:78874200-78884400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr4:78874800-78881200	Weak transcription	Brain Substantia Nigra	brain
21	chr4:78875200-78879200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:78875200-78881200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:78875200-78883800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr4:78875400-78881000	Weak transcription	HSMM	muscle
25	chr4:78875400-78884000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr4:78876000-78881000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:78876000-78881000	Weak transcription	Fetal Lung	lung
28	chr4:78876000-78883400	Weak transcription	Thymus	Thymus
29	chr4:78876000-78884000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr4:78876200-78880800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr4:78876200-78880800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr4:78876200-78880800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:78876200-78881000	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:78876200-78881000	Weak transcription	Aorta	Aorta
35	chr4:78876200-78881000	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr4:78876200-78881000	Weak transcription	Ovary	ovary
37	chr4:78876200-78881200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:78876200-78881200	Weak transcription	NH-A	brain
39	chr4:78876200-78884000	Weak transcription	Primary T cells from cord blood	blood
40	chr4:78876200-78884000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr4:78876200-78884200	Weak transcription	Fetal Thymus	thymus
42	chr4:78876400-78879400	Weak transcription	Primary B cells from cord blood	blood
43	chr4:78876400-78880800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:78876400-78881200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
45	chr4:78876600-78881200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr4:78877000-78880200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:78878000-78881000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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