Variant report

Variant	rs11789723
Chromosome Location	chr9:96036574-96036575
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95922407..95924638-chr9:96036435..96038460,2	MCF-7	breast:
2	chr9:96034754..96037251-chr9:96038032..96040798,2	MCF-7	breast:
3	chr9:95945425..95948152-chr9:96035262..96036926,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165238	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10992699	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12000967	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12002458	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12005950	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12006039	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13283550	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13289160	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35199621	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35566702	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs36081907	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55981123	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6479471	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6479474	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7022051	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7042943	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7848843	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7857220	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7867954	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96006200-96043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:96025600-96041200	Weak transcription	Psoas Muscle	Psoas
3	chr9:96027000-96036800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr9:96027200-96051200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:96027200-96056000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:96027200-96061000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr9:96031400-96037800	Weak transcription	Gastric	stomach
8	chr9:96031400-96054600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:96031400-96055000	Weak transcription	Colonic Mucosa	Colon
10	chr9:96031400-96062800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr9:96031600-96040400	Weak transcription	HepG2	liver
12	chr9:96032600-96043400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr9:96033000-96054600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr9:96033000-96055000	Weak transcription	Brain Anterior Caudate	brain
15	chr9:96033000-96067200	Weak transcription	Brain Angular Gyrus	brain
16	chr9:96033400-96062800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:96033400-96067000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr9:96033400-96077200	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr9:96033600-96044400	Weak transcription	Left Ventricle	heart
20	chr9:96033600-96046000	Weak transcription	Pancreas	Pancrea
21	chr9:96033600-96050200	Weak transcription	Fetal Intestine Small	intestine
22	chr9:96033600-96054600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr9:96033600-96060200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr9:96033600-96061000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr9:96033600-96072800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr9:96033800-96040400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr9:96033800-96040600	Weak transcription	Duodenum Mucosa	Duodenum
28	chr9:96033800-96054600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr9:96033800-96060400	Weak transcription	Colon Smooth Muscle	Colon
30	chr9:96034200-96040400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr9:96034400-96039800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr9:96034400-96040000	Weak transcription	Brain Germinal Matrix	brain
33	chr9:96035800-96051600	Weak transcription	Fetal Intestine Large	intestine
34	chr9:96036400-96039400	Weak transcription	Fetal Brain Female	brain
35	chr9:96036400-96039800	Weak transcription	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links