Variant report

Variant	rs9877045
Chromosome Location	chr3:49129625-49129626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49128910..49133326-chr3:49168969..49172072,7	MCF-7	breast:
2	chr3:49128213..49133667-chr3:49140039..49144982,11	MCF-7	breast:
3	chr3:49128926..49138937-chr3:49145476..49160975,31	K562	blood:
4	chr3:49129337..49131574-chr3:49165635..49167419,2	K562	blood:
5	chr3:49062154..49067981-chr3:49128951..49132856,8	K562	blood:
6	chr3:49129088..49132112-chr3:49168482..49170657,4	MCF-7	breast:
7	chr3:49055445..49060745-chr3:49128874..49135153,17	MCF-7	breast:
8	chr3:49052218..49068794-chr3:49126865..49133927,44	K562	blood:
9	chr3:49054288..49061452-chr3:49128946..49133927,24	K562	blood:
10	chr3:49128925..49131724-chr3:49157587..49160255,2	MCF-7	breast:
11	chr3:49062784..49068653-chr3:49129538..49133266,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000178149	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000207605	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000172053	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs13318132	1.00[EUR][1000 genomes]
rs14828	1.00[EUR][1000 genomes]
rs17080495	1.00[EUR][1000 genomes]
rs17080510	1.00[EUR][1000 genomes]
rs17080567	1.00[EUR][1000 genomes]
rs28523319	1.00[EUR][1000 genomes]
rs28615670	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4527417	1.00[EUR][1000 genomes]
rs55990645	1.00[EUR][1000 genomes]
rs56101322	1.00[EUR][1000 genomes]
rs56760510	1.00[EUR][1000 genomes]
rs56897974	1.00[EUR][1000 genomes]
rs58914641	1.00[EUR][1000 genomes]
rs58998762	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60011446	1.00[EUR][1000 genomes]
rs60338814	1.00[EUR][1000 genomes]
rs61008775	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61744082	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61749312	1.00[EUR][1000 genomes]
rs6766297	1.00[EUR][1000 genomes]
rs6787665	1.00[EUR][1000 genomes]
rs72930094	1.00[EUR][1000 genomes]
rs72931155	1.00[EUR][1000 genomes]
rs72931157	1.00[EUR][1000 genomes]
rs72931171	1.00[EUR][1000 genomes]
rs72934791	1.00[EUR][1000 genomes]
rs72936804	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72936810	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72936890	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830703	1.00[EUR][1000 genomes]
rs73830704	1.00[EUR][1000 genomes]
rs73830705	1.00[EUR][1000 genomes]
rs73830706	1.00[EUR][1000 genomes]
rs73833525	1.00[EUR][1000 genomes]
rs8179172	1.00[EUR][1000 genomes]
rs9811460	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9814413	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9820609	1.00[ASW][hapmap];0.88[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs9833422	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9837396	1.00[EUR][1000 genomes]
rs9849446	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9860187	1.00[EUR][1000 genomes]
rs9861805	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9869504	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9875203	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9876812	1.00[EUR][1000 genomes]
rs9882714	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers 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	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49066800-49130000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49066800-49130200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49114400-49129800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:49114400-49130000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr3:49115000-49130200	Weak transcription	Aorta	Aorta
6	chr3:49115000-49130600	Weak transcription	Spleen	Spleen
7	chr3:49115600-49130000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:49115600-49130200	Weak transcription	Esophagus	oesophagus
9	chr3:49116000-49129800	Weak transcription	Colonic Mucosa	Colon
10	chr3:49116800-49130200	Weak transcription	Placenta	Placenta
11	chr3:49117200-49130000	Weak transcription	Right Atrium	heart
12	chr3:49117200-49130200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:49117200-49130200	Weak transcription	Gastric	stomach
14	chr3:49117200-49130400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:49119600-49130200	Weak transcription	Lung	lung
16	chr3:49119600-49130200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:49122200-49130200	Weak transcription	Left Ventricle	heart
18	chr3:49124200-49130200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr3:49125800-49130000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr3:49126200-49130000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:49126200-49130000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:49126200-49130400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:49126800-49130000	Enhancers	Brain Angular Gyrus	brain
24	chr3:49126800-49130200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:49126800-49130200	Weak transcription	Ovary	ovary
26	chr3:49127000-49129800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:49127400-49129800	Enhancers	Liver	Liver
28	chr3:49128000-49130000	Genic enhancers	Primary B cells from peripheral blood	blood
29	chr3:49128000-49130000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr3:49128200-49130000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr3:49128200-49130000	Enhancers	Fetal Brain Male	brain
32	chr3:49128400-49129800	Enhancers	Primary B cells from cord blood	blood
33	chr3:49128400-49129800	Enhancers	Adipose Nuclei	Adipose
34	chr3:49128400-49130000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr3:49128400-49130000	Enhancers	Brain Hippocampus Middle	brain
36	chr3:49128400-49130000	Enhancers	Small Intestine	intestine
37	chr3:49128600-49129800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr3:49128600-49129800	Genic enhancers	Primary T cells from cord blood	blood
39	chr3:49128600-49130000	Genic enhancers	Fetal Muscle Leg	muscle
40	chr3:49128600-49130200	Weak transcription	Pancreas	Pancrea
41	chr3:49128800-49129800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr3:49128800-49129800	Genic enhancers	Primary monocytes fromperipheralblood	blood
43	chr3:49128800-49129800	Genic enhancers	Fetal Stomach	stomach
44	chr3:49128800-49130000	Enhancers	Thymus	Thymus
45	chr3:49128800-49130200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr3:49129000-49130000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:49129000-49130000	Weak transcription	Colon Smooth Muscle	Colon
48	chr3:49129000-49130000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
49	chr3:49129000-49130200	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr3:49129000-49130200	Enhancers	Primary T cells fromperipheralblood	blood

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