Variant report

Variant	rs11790978
Chromosome Location	chr9:22216238-22216239
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:22139628..22142458-chr9:22215449..22217635,2	MCF-7	breast:
2	chr9:22216075..22219047-chr9:22230410..22232299,2	MCF-7	breast:
3	chr9:22007424..22010079-chr9:22214224..22216298,2	MCF-7	breast:
4	chr9:22101148..22103535-chr9:22215387..22218852,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147883	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11788928	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11792798	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11792897	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11792932	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12003808	0.90[EUR][1000 genomes]
rs16905769	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2025797	0.90[EUR][1000 genomes]
rs2383209	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2383212	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2383213	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4461984	0.90[EUR][1000 genomes]
rs4644346	0.95[EUR][1000 genomes]
rs62555449	0.95[EUR][1000 genomes]
rs62555450	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62555451	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62555452	0.95[EUR][1000 genomes]
rs62555453	0.90[EUR][1000 genomes]
rs62555455	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62559460	0.95[EUR][1000 genomes]
rs62559467	0.95[EUR][1000 genomes]
rs62559468	0.90[EUR][1000 genomes]
rs62559469	0.95[EUR][1000 genomes]
rs62559470	0.95[EUR][1000 genomes]
rs62559471	0.95[EUR][1000 genomes]
rs62559472	0.86[EUR][1000 genomes]
rs62559473	0.86[EUR][1000 genomes]
rs62559474	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62559475	0.86[EUR][1000 genomes]
rs62559494	0.82[EUR][1000 genomes]
rs62559495	0.82[EUR][1000 genomes]
rs6475620	0.90[EUR][1000 genomes]
rs7035115	0.90[EUR][1000 genomes]
rs73442947	0.90[EUR][1000 genomes]
rs73444955	0.95[EUR][1000 genomes]
rs736723	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7848967	0.90[EUR][1000 genomes]
rs7853527	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7853566	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7859353	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7859407	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7872728	0.85[EUR][1000 genomes]
rs943399	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529609	chr9:21708371-22537069	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv531617	chr9:21985057-22809676	Genic enhancers Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv892749	chr9:22125913-22244280	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1021264	chr9:22159622-22293804	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1033789	chr9:22183150-22266091	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1029289	chr9:22193167-23023688	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1016067	chr9:22210874-22432654	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1015364	chr9:22211364-22416886	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv540086	chr9:22211364-22416886	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:22200800-22216600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:22208600-22217200	Enhancers	HSMMtube	muscle
3	chr9:22208800-22218000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr9:22209400-22216400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:22209400-22216800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr9:22209400-22217000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:22209400-22217600	Enhancers	NHDF-Ad	bronchial
8	chr9:22209400-22218400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:22209600-22216600	Enhancers	Hela-S3	cervix
10	chr9:22212800-22220200	Strong transcription	A549	lung
11	chr9:22213000-22216800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr9:22214200-22217600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:22214600-22216600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr9:22214800-22216600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:22215000-22216600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr9:22215000-22216600	Weak transcription	HSMM	muscle
17	chr9:22215200-22216400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr9:22215200-22216600	Weak transcription	Osteobl	bone
19	chr9:22215200-22216800	Weak transcription	HMEC	breast
20	chr9:22215200-22216800	Weak transcription	NH-A	brain
21	chr9:22215200-22216800	Weak transcription	NHLF	lung
22	chr9:22215200-22219000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:22215600-22217000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:22216200-22217800	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links