Variant report

Variant	rs1923599
Chromosome Location	chr9:95092568-95092569
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95088163..95089676-chr9:95089853..95092635,2	MCF-7	breast:
2	chr9:95090696..95092627-chr9:95093724..95096135,2	K562	blood:
3	chr9:95087133..95088764-chr9:95090967..95092717,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198000	Chromatin interaction
ENSG00000188312	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10761149	0.89[CEU][hapmap]
rs10761156	0.92[CEU][hapmap]
rs10820952	0.89[CEU][hapmap]
rs1152757	0.89[CEU][hapmap]
rs1152759	0.93[CEU][hapmap]
rs1175788	0.92[CEU][hapmap]
rs1760318	0.85[CEU][hapmap]
rs2025389	0.93[CEU][hapmap]
rs2031262	0.93[CEU][hapmap]
rs2147060	0.93[CEU][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs230222	0.93[CEU][hapmap]
rs3174352	0.93[CEU][hapmap]
rs331377	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs331379	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs331380	0.93[CEU][hapmap]
rs331381	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3736835	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3780346	0.82[CEU][hapmap]
rs3996311	0.89[CEU][hapmap]
rs471478	0.89[CEU][hapmap]
rs4743869	0.89[CEU][hapmap]
rs544396	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6651532	0.89[CEU][hapmap]
rs7048808	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs710163	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7867300	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs9299402	0.83[EUR][1000 genomes]
rs9409664	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv893573	chr9:94974188-95355719	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1045165	chr9:95057462-95138564	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95088600-95096800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:95088600-95100000	Weak transcription	Spleen	Spleen
3	chr9:95088600-95101000	Weak transcription	Aorta	Aorta
4	chr9:95088600-95103600	Weak transcription	Esophagus	oesophagus
5	chr9:95088600-95104000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr9:95088600-95108600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:95088800-95099800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:95088800-95100000	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr9:95088800-95100000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr9:95088800-95100000	Weak transcription	Lung	lung
11	chr9:95088800-95100200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:95088800-95100400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr9:95088800-95100400	Weak transcription	Ovary	ovary
14	chr9:95088800-95102000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:95088800-95102600	Weak transcription	Small Intestine	intestine
16	chr9:95088800-95103600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr9:95088800-95103800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr9:95088800-95103800	Weak transcription	Pancreas	Pancrea
19	chr9:95088800-95104000	Weak transcription	Left Ventricle	heart
20	chr9:95088800-95111200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:95088800-95111600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:95089000-95097000	Weak transcription	Psoas Muscle	Psoas
23	chr9:95089000-95099800	Weak transcription	Primary B cells from cord blood	blood
24	chr9:95089000-95100000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr9:95089000-95100000	Weak transcription	Brain Angular Gyrus	brain
26	chr9:95089000-95100000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr9:95089000-95101000	Weak transcription	Brain Substantia Nigra	brain
28	chr9:95089000-95101200	Weak transcription	Brain Cingulate Gyrus	brain
29	chr9:95089000-95101400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:95089000-95102000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr9:95089000-95102600	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr9:95089000-95103200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr9:95089000-95103600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr9:95089000-95104000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr9:95089000-95104000	Weak transcription	HSMMtube	muscle
36	chr9:95089000-95105600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:95089000-95110200	Weak transcription	HSMM	muscle
38	chr9:95089000-95112200	Weak transcription	Adipose Nuclei	Adipose
39	chr9:95089200-95097800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr9:95089200-95099800	Weak transcription	Brain Anterior Caudate	brain
41	chr9:95089200-95100000	Weak transcription	Liver	Liver
42	chr9:95089200-95100000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr9:95089200-95100000	Weak transcription	Fetal Brain Female	brain
44	chr9:95089200-95100600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr9:95089200-95101800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr9:95089200-95103800	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr9:95089200-95110000	Weak transcription	Brain Hippocampus Middle	brain
48	chr9:95089400-95096600	Weak transcription	Fetal Intestine Small	intestine
49	chr9:95089400-95098600	Weak transcription	Primary T cells from cord blood	blood
50	chr9:95089400-95098800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links