Variant report

Variant	rs28464341
Chromosome Location	chr9:96303978-96303979
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96302153..96304744-chr9:96309522..96311338,2	MCF-7	breast:
2	chr9:96303519..96305810-chr9:96307510..96309071,2	K562	blood:
3	chr9:96212589..96215619-chr9:96298935..96305511,9	MCF-7	breast:
4	chr9:96302294..96305267-chr9:96306337..96308458,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188938	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10116959	1.00[EUR][1000 genomes]
rs10117404	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10118281	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10118574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10118955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10121548	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10121798	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10122307	0.80[AFR][1000 genomes]
rs10123186	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10123412	1.00[EUR][1000 genomes]
rs10125504	0.83[AFR][1000 genomes]
rs10992753	0.83[AFR][1000 genomes]
rs10992758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10992822	1.00[EUR][1000 genomes]
rs1123475	1.00[EUR][1000 genomes]
rs12337821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12340447	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12344186	1.00[EUR][1000 genomes]
rs12346586	1.00[EUR][1000 genomes]
rs12348843	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12349453	1.00[EUR][1000 genomes]
rs16909307	1.00[EUR][1000 genomes]
rs28406634	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28523540	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28630935	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28666855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28728320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58925215	1.00[EUR][1000 genomes]
rs61301026	1.00[EUR][1000 genomes]
rs61467488	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61636268	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7021423	1.00[EUR][1000 genomes]
rs7022246	1.00[EUR][1000 genomes]
rs7033089	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73651245	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73651251	1.00[EUR][1000 genomes]
rs73651269	1.00[EUR][1000 genomes]
rs73651270	1.00[EUR][1000 genomes]
rs73651296	1.00[AMR][1000 genomes]
rs73651297	1.00[EUR][1000 genomes]
rs73651298	1.00[EUR][1000 genomes]
rs7848429	1.00[EUR][1000 genomes]
rs7850596	1.00[EUR][1000 genomes]
rs7854758	1.00[EUR][1000 genomes]
rs7856259	1.00[EUR][1000 genomes]
rs7870048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7871486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041803	chr9:96299639-96342013	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96278400-96310800	Strong transcription	Rectal Mucosa Donor 31	rectum
2	chr9:96278400-96327000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr9:96278400-96327200	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr9:96278400-96328200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr9:96278600-96311200	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr9:96279000-96310400	Strong transcription	Primary B cells from peripheral blood	blood
7	chr9:96279000-96327400	Strong transcription	Primary T helper cells fromperipheralblood	blood
8	chr9:96282200-96323400	Strong transcription	Primary B cells from cord blood	blood
9	chr9:96284600-96327200	Strong transcription	Primary T helper cells PMA-I stimulated	--
10	chr9:96284600-96328200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:96284800-96309800	Strong transcription	Duodenum Mucosa	Duodenum
12	chr9:96284800-96327200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:96285000-96304000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr9:96285000-96327000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr9:96285000-96327000	Strong transcription	Dnd41	blood
16	chr9:96285200-96327800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr9:96285400-96304200	Strong transcription	HSMM	muscle
18	chr9:96285400-96327800	Strong transcription	Liver	Liver
19	chr9:96285600-96310000	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr9:96286000-96304000	Strong transcription	Adipose Nuclei	Adipose
21	chr9:96288600-96304200	Strong transcription	K562	blood
22	chr9:96289200-96316000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:96291600-96305400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:96291800-96317000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr9:96291800-96317000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:96292000-96316600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr9:96292800-96310000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr9:96293000-96310400	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr9:96293200-96309600	Strong transcription	Primary hematopoietic stem cells	blood
30	chr9:96295000-96305200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:96295200-96306200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:96295200-96308600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr9:96295600-96305600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr9:96295800-96307600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr9:96295800-96315600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr9:96296000-96305600	Weak transcription	Fetal Kidney	kidney
37	chr9:96296200-96305400	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr9:96296400-96304000	Weak transcription	Colon Smooth Muscle	Colon
39	chr9:96296400-96305400	Weak transcription	Brain Anterior Caudate	brain
40	chr9:96296400-96305400	Weak transcription	Brain Germinal Matrix	brain
41	chr9:96296400-96306200	Weak transcription	Aorta	Aorta
42	chr9:96296600-96305400	Weak transcription	Fetal Brain Female	brain
43	chr9:96296600-96306200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:96297800-96305200	Weak transcription	NHDF-Ad	bronchial
45	chr9:96297800-96310400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:96298200-96304600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr9:96298200-96304600	Strong transcription	Fetal Intestine Small	intestine
48	chr9:96298200-96309800	Strong transcription	Fetal Stomach	stomach
49	chr9:96298600-96306200	Weak transcription	Small Intestine	intestine
50	chr9:96298800-96304000	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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