Variant report

Variant	rs6477999
Chromosome Location	chr9:115998792-115998793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:115990891..115993253-chr9:115993931..115999009,4	K562	blood:
2	chr9:115995531..115997450-chr9:115998162..116001080,2	MCF-7	breast:
3	chr9:115996965..115999527-chr9:116002148..116004164,2	K562	blood:
4	chr9:115982366..115985193-chr9:115997022..116000102,3	MCF-7	breast:
5	chr9:115988089..115990143-chr9:115997118..115999123,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119321	Chromatin interaction
ENSG00000136868	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10123415	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10125992	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10513189	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10739388	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10739390	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10739392	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10759633	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10759636	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10759637	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10817461	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10817468	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11792628	0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4129395	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4129396	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4129397	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4284098	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4560868	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4979223	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4979226	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6477998	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7022397	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7038769	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7041615	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7850357	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7851395	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7859354	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][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	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv1035406	chr9:115883978-116003980	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv540201	chr9:115883978-116003980	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv893745	chr9:115955271-116005783	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1041112	chr9:115960704-116005783	Weak transcription Flanking Active TSS Strong transcription Enhancers 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	9 gene(s)	inside rSNPs	diseases
10	nsv893746	chr9:115983540-116022826	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6477999	CDC26	cis	Esophagus Muscularis	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115985000-116020800	Weak transcription	Aorta	Aorta
2	chr9:115985200-116001800	Weak transcription	Pancreas	Pancrea
3	chr9:115985600-116020800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:115985800-116018400	Weak transcription	NHEK	skin
5	chr9:115985800-116019000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr9:115985800-116021000	Weak transcription	Fetal Stomach	stomach
7	chr9:115986400-116013000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:115987600-116017800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr9:115987600-116018200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr9:115987800-116011000	Weak transcription	A549	lung
11	chr9:115987800-116021000	Weak transcription	Hela-S3	cervix
12	chr9:115989000-116019200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:115989200-116005600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr9:115991000-116011600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:115995200-116017800	Weak transcription	Left Ventricle	heart
16	chr9:115995400-116009200	Weak transcription	K562	blood
17	chr9:115995400-116018000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:115995800-115999400	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr9:115995800-116005200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:115996000-115999200	Weak transcription	HepG2	liver
21	chr9:115996000-115999400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr9:115996000-116022200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr9:115996000-116031600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr9:115996200-115999000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr9:115996200-116018600	Weak transcription	Primary T cells from cord blood	blood
26	chr9:115996200-116022400	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr9:115996400-116000600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:115996400-116003200	Enhancers	Liver	Liver
29	chr9:115996600-116019200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:115998200-115999600	Weak transcription	Small Intestine	intestine
31	chr9:115998200-116001000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr9:115998400-115999000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr9:115998400-116000200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:115998400-116018200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:115998600-116000800	Weak transcription	Adipose Nuclei	Adipose
36	chr9:115998600-116013000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links