Variant report

Variant	rs56364682
Chromosome Location	chr2:110321230-110321231
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	chr2:110315553..110317822-chr2:110320975..110322550,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10175432	0.90[ASN][1000 genomes]
rs11541143	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12998808	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2018352	0.94[ASN][1000 genomes]
rs2043462	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2060402	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2060403	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28369323	0.82[ASN][1000 genomes]
rs28544318	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28567471	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28583991	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28615410	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28728215	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34557890	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923006	0.95[ASN][1000 genomes]
rs3934873	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4953760	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953784	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4953843	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4953850	0.84[ASN][1000 genomes]
rs56402128	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58012425	0.81[ASN][1000 genomes]
rs61215808	0.82[ASN][1000 genomes]
rs6594037	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6594049	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6716287	0.82[ASN][1000 genomes]
rs6723295	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6726252	0.95[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6745809	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6748632	0.83[ASN][1000 genomes]
rs72938271	0.81[ASN][1000 genomes]
rs747445	0.94[ASN][1000 genomes]
rs7596172	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs767628	0.82[ASN][1000 genomes]
rs892460	0.94[ASN][1000 genomes]
rs919941	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9330311	0.88[ASN][1000 genomes]
rs9330320	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9330324	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[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
rs56364682	SEPT10	cis	Muscle Skeletal	GTEx

Chromatin state (count:94 , 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	chr2:110307200-110322800	Weak transcription	Brain Anterior Caudate	brain
11	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
13	chr2:110309000-110347400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr2:110309800-110323000	Weak transcription	Aorta	Aorta
15	chr2:110309800-110351600	Weak transcription	Pancreas	Pancrea
16	chr2:110310200-110351600	Weak transcription	Fetal Brain Male	brain
17	chr2:110310400-110323000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr2:110310400-110323000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr2:110310400-110337800	Weak transcription	Brain Cingulate Gyrus	brain
20	chr2:110310400-110338400	Weak transcription	Lung	lung
21	chr2:110310400-110342000	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:110310400-110351600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:110310400-110351800	Weak transcription	Fetal Brain Female	brain
24	chr2:110310400-110353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:110310600-110341400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:110310800-110336800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:110312200-110321400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr2:110312200-110326000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:110312200-110328400	Weak transcription	Ovary	ovary
31	chr2:110313000-110321400	Weak transcription	Fetal Intestine Large	intestine
32	chr2:110313400-110325200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr2:110313400-110337000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:110313600-110323000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr2:110315200-110322800	Weak transcription	Adipose Nuclei	Adipose
36	chr2:110315400-110324000	Strong transcription	Fetal Stomach	stomach
37	chr2:110316000-110323200	Weak transcription	Duodenum Mucosa	Duodenum
38	chr2:110316200-110324000	Weak transcription	Fetal Kidney	kidney
39	chr2:110317000-110325000	Strong transcription	Fetal Lung	lung
40	chr2:110317000-110326800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr2:110317200-110323000	Weak transcription	Left Ventricle	heart
42	chr2:110317400-110321600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:110317400-110322200	Weak transcription	Hela-S3	cervix
44	chr2:110317400-110323000	Weak transcription	GM12878-XiMat	blood
45	chr2:110317800-110322400	Enhancers	Osteobl	bone
46	chr2:110318000-110321800	Weak transcription	HSMM	muscle
47	chr2:110318200-110325400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:110318200-110338000	Weak transcription	NHEK	skin
49	chr2:110318200-110348400	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:110318400-110324800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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