Variant report

Variant	rs28728215
Chromosome Location	chr2:110306340-110306341
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:110306100..110309560-chr2:110371773..110373561,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198142	Chromatin interaction
ENSG00000186522	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10175432	0.90[ASN][1000 genomes]
rs11541143	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12998808	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2018352	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2043462	0.91[ASN][1000 genomes]
rs2060402	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2060403	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28544318	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28567471	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28583991	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28615410	0.93[ASN][1000 genomes]
rs34557890	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3923006	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3934873	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4953760	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4953784	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4953843	0.90[ASN][1000 genomes]
rs4953850	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56364682	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56402128	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58012425	0.81[ASN][1000 genomes]
rs6594037	0.94[ASN][1000 genomes]
rs6594049	0.81[ASN][1000 genomes]
rs6723295	0.91[ASN][1000 genomes]
rs6726252	0.81[ASN][1000 genomes]
rs6745809	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748632	0.87[AMR][1000 genomes]
rs747445	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7596172	0.94[ASN][1000 genomes]
rs892460	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs919941	0.90[ASN][1000 genomes]
rs9330311	0.88[ASN][1000 genomes]
rs9330320	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9330324	0.82[EUR][1000 genomes];0.94[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	nsv874777	chr2:109825516-110693317	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv874780	chr2:110078080-110432886	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv2874	chr2:110289373-110333621	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1011456	chr2:110290958-110980402	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv535861	chr2:110290958-110980402	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv482469	chr2:110302488-110452580	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28728215	SEPT10	cis	Muscle Skeletal	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110291000-110309400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:110291800-110309400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:110293200-110316200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:110293400-110309400	Weak transcription	Left Ventricle	heart
5	chr2:110293400-110309600	Weak transcription	Lung	lung
6	chr2:110293400-110309600	Weak transcription	NHDF-Ad	bronchial
7	chr2:110293400-110331600	Weak transcription	Right Ventricle	heart
8	chr2:110293400-110352200	Weak transcription	Gastric	stomach
9	chr2:110293600-110309400	Weak transcription	Liver	Liver
10	chr2:110296000-110312200	Weak transcription	Stomach Mucosa	stomach
11	chr2:110296400-110309400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:110296400-110309400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:110296400-110309400	Weak transcription	HSMMtube	muscle
14	chr2:110296400-110313400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:110296800-110309400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:110297400-110351600	Weak transcription	Brain Germinal Matrix	brain
17	chr2:110297800-110331800	Weak transcription	Colonic Mucosa	Colon
18	chr2:110298000-110309200	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:110298000-110310200	Weak transcription	Hela-S3	cervix
20	chr2:110298400-110309600	Weak transcription	Ovary	ovary
21	chr2:110299600-110309400	Weak transcription	Aorta	Aorta
22	chr2:110299600-110309600	Weak transcription	Pancreas	Pancrea
23	chr2:110299600-110318600	Weak transcription	Esophagus	oesophagus
24	chr2:110299600-110320200	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr2:110299600-110324200	Weak transcription	Brain Angular Gyrus	brain
26	chr2:110299800-110309600	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr2:110300200-110309400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:110300200-110309600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr2:110300200-110309600	Weak transcription	Stomach Smooth Muscle	stomach
30	chr2:110301000-110309600	Weak transcription	Brain Hippocampus Middle	brain
31	chr2:110301000-110310000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr2:110301400-110325000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr2:110301600-110321000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:110301800-110309600	Weak transcription	Fetal Brain Female	brain
35	chr2:110301800-110309600	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:110302000-110333600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:110302400-110343000	Weak transcription	Psoas Muscle	Psoas
39	chr2:110303000-110320400	Weak transcription	Brain Substantia Nigra	brain
40	chr2:110303400-110306800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr2:110303400-110306800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr2:110303400-110308600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:110303600-110306400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:110303600-110308000	Weak transcription	HSMM	muscle
45	chr2:110303600-110308200	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr2:110303600-110308400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:110303600-110308600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr2:110303600-110308600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr2:110303600-110309000	Weak transcription	Fetal Intestine Large	intestine
50	chr2:110303600-110309000	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links