Variant report

Variant	rs28544318
Chromosome Location	chr2:110323694-110323695
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10175432	0.90[ASN][1000 genomes]
rs11541143	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12998808	0.92[ASN][1000 genomes]
rs2018352	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2043462	0.94[ASN][1000 genomes]
rs2060402	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060403	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28369323	0.82[ASN][1000 genomes]
rs28567471	0.98[ASN][1000 genomes]
rs28583991	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28615410	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28728215	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34557890	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829700	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3923006	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3934873	0.93[ASN][1000 genomes]
rs4953760	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953784	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953843	0.94[ASN][1000 genomes]
rs4953850	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56364682	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56402128	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58012425	0.81[ASN][1000 genomes]
rs61215808	0.82[ASN][1000 genomes]
rs6594037	0.97[ASN][1000 genomes]
rs6594049	0.84[ASN][1000 genomes]
rs6716287	0.82[ASN][1000 genomes]
rs6723295	0.94[ASN][1000 genomes]
rs6726252	0.84[ASN][1000 genomes]
rs6745809	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748632	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72938271	0.81[ASN][1000 genomes]
rs747445	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7596172	0.97[ASN][1000 genomes]
rs767628	0.82[ASN][1000 genomes]
rs892460	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs919941	0.93[ASN][1000 genomes]
rs9330311	0.88[ASN][1000 genomes]
rs9330320	0.93[ASN][1000 genomes]
rs9330324	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
rs28544318	SEPT10	cis	Muscle Skeletal	GTEx

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110293400-110331600	Weak transcription	Right Ventricle	heart
2	chr2:110293400-110352200	Weak transcription	Gastric	stomach
3	chr2:110297400-110351600	Weak transcription	Brain Germinal Matrix	brain
4	chr2:110297800-110331800	Weak transcription	Colonic Mucosa	Colon
5	chr2:110299600-110324200	Weak transcription	Brain Angular Gyrus	brain
6	chr2:110301400-110325000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:110302000-110333600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr2:110302400-110343000	Weak transcription	Psoas Muscle	Psoas
10	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
12	chr2:110309000-110347400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:110309800-110351600	Weak transcription	Pancreas	Pancrea
14	chr2:110310200-110351600	Weak transcription	Fetal Brain Male	brain
15	chr2:110310400-110337800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:110310400-110338400	Weak transcription	Lung	lung
17	chr2:110310400-110342000	Weak transcription	Brain Hippocampus Middle	brain
18	chr2:110310400-110351600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:110310400-110351800	Weak transcription	Fetal Brain Female	brain
20	chr2:110310400-110353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:110310600-110341400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:110310800-110336800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:110312200-110326000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr2:110312200-110328400	Weak transcription	Ovary	ovary
26	chr2:110313400-110325200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:110313400-110337000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr2:110315400-110324000	Strong transcription	Fetal Stomach	stomach
29	chr2:110316200-110324000	Weak transcription	Fetal Kidney	kidney
30	chr2:110317000-110325000	Strong transcription	Fetal Lung	lung
31	chr2:110317000-110326800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr2:110318200-110325400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr2:110318200-110338000	Weak transcription	NHEK	skin
34	chr2:110318200-110348400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr2:110318400-110324800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr2:110318800-110328200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr2:110319200-110367400	Weak transcription	HSMMtube	muscle
38	chr2:110319400-110358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:110319600-110325600	Strong transcription	Liver	Liver
40	chr2:110319800-110325800	Strong transcription	Stomach Smooth Muscle	stomach
41	chr2:110320000-110326000	Strong transcription	HepG2	liver
42	chr2:110320200-110324000	Strong transcription	Fetal Intestine Small	intestine
43	chr2:110320200-110324600	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:110320200-110325000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:110320200-110325400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:110320200-110325600	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr2:110320200-110326200	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr2:110320400-110325400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:110320600-110354600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:110320800-110325400	Strong transcription	Duodenum Smooth Muscle	Duodenum

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