Variant report

Variant	rs3793546
Chromosome Location	chr9:96055671-96055672
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	chr9:96050880..96053674-chr9:96053740..96056815,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165238	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10761201	0.83[EUR][1000 genomes]
rs10761203	0.94[ASN][1000 genomes]
rs10761204	0.85[EUR][1000 genomes]
rs10761205	0.85[EUR][1000 genomes]
rs10761209	0.85[EUR][1000 genomes]
rs10821095	0.90[ASN][1000 genomes]
rs10821096	0.82[EUR][1000 genomes]
rs10821097	0.82[EUR][1000 genomes]
rs10821098	0.93[ASN][1000 genomes]
rs10821099	0.84[EUR][1000 genomes]
rs10821100	0.84[EUR][1000 genomes]
rs10821101	0.84[EUR][1000 genomes]
rs10821105	0.88[EUR][1000 genomes]
rs10821106	0.87[EUR][1000 genomes]
rs10992689	0.83[EUR][1000 genomes]
rs10992697	0.85[EUR][1000 genomes]
rs10992698	0.93[ASN][1000 genomes]
rs10992702	0.90[ASN][1000 genomes]
rs10992704	0.82[EUR][1000 genomes]
rs1110335	0.84[EUR][1000 genomes]
rs12341303	0.90[ASN][1000 genomes]
rs12684394	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1317698	0.95[ASN][1000 genomes]
rs13292831	0.94[ASN][1000 genomes]
rs13293217	0.85[ASN][1000 genomes]
rs1463544	0.85[EUR][1000 genomes]
rs2012744	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2086103	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306183	0.95[ASN][1000 genomes]
rs2398822	0.90[ASN][1000 genomes]
rs35795732	0.93[ASN][1000 genomes]
rs3763634	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3763635	0.95[ASN][1000 genomes]
rs41278286	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4743905	0.85[EUR][1000 genomes]
rs4743911	0.95[ASN][1000 genomes]
rs4744195	0.86[ASN][1000 genomes]
rs4744201	0.94[ASN][1000 genomes]
rs4744203	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4744206	0.93[ASN][1000 genomes]
rs4744207	0.84[EUR][1000 genomes]
rs4744208	0.85[EUR][1000 genomes]
rs4744212	0.93[ASN][1000 genomes]
rs4744215	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7868971	0.86[ASN][1000 genomes]
rs944993	0.95[ASN][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:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96027200-96056000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr9:96027200-96061000	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr9:96031400-96062800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:96033000-96067200	Weak transcription	Brain Angular Gyrus	brain
5	chr9:96033400-96062800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr9:96033400-96067000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr9:96033400-96077200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr9:96033600-96060200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr9:96033600-96061000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr9:96033600-96072800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr9:96033800-96060400	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:96041600-96056800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr9:96047200-96065000	Weak transcription	Fetal Brain Male	brain
14	chr9:96048200-96057200	Weak transcription	Right Atrium	heart
15	chr9:96049200-96057600	Strong transcription	Fetal Brain Female	brain
16	chr9:96049400-96057000	Strong transcription	Brain Germinal Matrix	brain
17	chr9:96050000-96056600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr9:96050200-96056800	Strong transcription	Fetal Intestine Small	intestine
19	chr9:96051000-96056600	Weak transcription	Left Ventricle	heart
20	chr9:96051200-96056200	Weak transcription	Fetal Heart	heart
21	chr9:96051400-96056400	Weak transcription	Spleen	Spleen
22	chr9:96051400-96067800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:96052000-96056800	Strong transcription	Fetal Intestine Large	intestine
24	chr9:96052000-96060800	Weak transcription	Placenta	Placenta
25	chr9:96052200-96056600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:96052200-96066600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:96052400-96057400	Strong transcription	Stomach Smooth Muscle	stomach
28	chr9:96052800-96056200	Weak transcription	HepG2	liver
29	chr9:96054400-96058200	Weak transcription	Brain Hippocampus Middle	brain
30	chr9:96054600-96056000	Strong transcription	Rectal Smooth Muscle	rectum
31	chr9:96054600-96056200	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr9:96054600-96056400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr9:96054600-96056400	Weak transcription	Thymus	Thymus
34	chr9:96054600-96056800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:96054800-96056600	Weak transcription	Fetal Thymus	thymus
36	chr9:96055000-96056800	Strong transcription	Brain Anterior Caudate	brain
37	chr9:96055200-96060200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr9:96055400-96056400	Weak transcription	Right Ventricle	heart
39	chr9:96055400-96057000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:96055400-96057200	Weak transcription	Colonic Mucosa	Colon
41	chr9:96055400-96057200	Weak transcription	Gastric	stomach
42	chr9:96055600-96056200	Weak transcription	Pancreas	Pancrea
43	chr9:96055600-96056400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr9:96055600-96056400	Weak transcription	Fetal Stomach	stomach
45	chr9:96055600-96056600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr9:96055600-96080200	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links