Variant report

Variant	rs4979454
Chromosome Location	chr9:117456175-117456176
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117455344..117457782-chr9:117461706..117463500,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10513257	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10817665	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10817666	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10817667	0.88[ASW][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10817668	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10982367	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10982370	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10982372	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1410561	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1557220	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1831177	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2149370	1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2296947	0.82[ASN][1000 genomes]
rs2418316	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4979449	0.81[ASN][1000 genomes]
rs4979453	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7022339	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7039257	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7847092	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7850949	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7868007	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7869653	0.92[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.83[YRI][hapmap];0.83[ASN][1000 genomes]
rs9886907	0.87[JPT][hapmap];0.88[MEX][hapmap]

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	nsv1048093	chr9:116945025-117456210	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
2	nsv1052877	chr9:116953739-117456210	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv1039681	chr9:116953739-117457158	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
4	nsv1044374	chr9:116955841-117460150	Genic enhancers Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv1048817	chr9:116957958-117456210	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
6	nsv466535	chr9:116958144-117456175	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
7	nsv615237	chr9:116958144-117456175	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
8	nsv615238	chr9:116958144-117458475	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
9	nsv430094	chr9:116958446-117456446	Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
10	nsv831694	chr9:117328640-117502785	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
11	nsv893766	chr9:117385992-117516418	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active 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
12	nsv1042718	chr9:117435306-117488969	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117452600-117457600	Enhancers	NHDF-Ad	bronchial
2	chr9:117453600-117457600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:117454000-117457400	Enhancers	HSMMtube	muscle
4	chr9:117454000-117457600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:117454000-117457600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:117454000-117457600	Enhancers	HMEC	breast
7	chr9:117454000-117459000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr9:117454000-117459000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:117454200-117456200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:117454200-117456400	Weak transcription	HUVEC	blood vessel
11	chr9:117454200-117459600	Weak transcription	Hela-S3	cervix
12	chr9:117454400-117458200	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr9:117454600-117456600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:117454600-117456600	Weak transcription	Osteobl	bone
15	chr9:117454600-117458800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr9:117454600-117458800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr9:117454600-117459200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr9:117454800-117458800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr9:117454800-117459000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr9:117455000-117459000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr9:117455200-117456600	Enhancers	Fetal Lung	lung
22	chr9:117455200-117457200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr9:117455200-117457200	Enhancers	NHLF	lung
24	chr9:117455200-117457400	Enhancers	NHEK	skin
25	chr9:117455400-117457000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr9:117455600-117456600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr9:117455600-117457200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr9:117455800-117456200	Enhancers	Small Intestine	intestine
29	chr9:117455800-117456400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr9:117455800-117456800	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr9:117455800-117457400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:117455800-117457600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:117455800-117457600	Enhancers	HSMM	muscle
34	chr9:117456000-117456600	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr9:117456000-117457200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr9:117456000-117457600	Enhancers	Muscle Satellite Cultured Cells	--
37	chr9:117456000-117457600	Enhancers	NH-A	brain

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