Variant report

Variant	rs2060402
Chromosome Location	chr2:110329104-110329105
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:110328393-110330192	A549	lung:	n/a	n/a

Variant related genes	Relation type
SEPT10	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

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

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:110293400-110331600	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	chr2:110302000-110333600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:110302400-110343000	Weak transcription	Psoas Muscle	Psoas
8	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
10	chr2:110309000-110347400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:110309800-110351600	Weak transcription	Pancreas	Pancrea
12	chr2:110310200-110351600	Weak transcription	Fetal Brain Male	brain
13	chr2:110310400-110337800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:110310400-110338400	Weak transcription	Lung	lung
15	chr2:110310400-110342000	Weak transcription	Brain Hippocampus Middle	brain
16	chr2:110310400-110351600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr2:110310400-110351800	Weak transcription	Fetal Brain Female	brain
18	chr2:110310400-110353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:110310600-110341400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:110310800-110336800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:110313400-110337000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr2:110318200-110338000	Weak transcription	NHEK	skin
24	chr2:110318200-110348400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr2:110319200-110367400	Weak transcription	HSMMtube	muscle
26	chr2:110319400-110358200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr2:110320600-110354600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:110321200-110332800	Weak transcription	Fetal Heart	heart
29	chr2:110323400-110331000	Weak transcription	HUVEC	blood vessel
30	chr2:110323400-110332600	Weak transcription	Brain Substantia Nigra	brain
31	chr2:110323400-110343800	Weak transcription	Aorta	Aorta
32	chr2:110323400-110348000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr2:110323400-110348200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr2:110323600-110330800	Weak transcription	Left Ventricle	heart
35	chr2:110323600-110341000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr2:110323600-110344200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:110324000-110337400	Weak transcription	Fetal Intestine Small	intestine
38	chr2:110324000-110342800	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr2:110324000-110348400	Weak transcription	Hela-S3	cervix
40	chr2:110324000-110370400	Weak transcription	Esophagus	oesophagus
41	chr2:110324200-110342800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:110324200-110348600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr2:110324600-110362200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr2:110325000-110330600	Weak transcription	Fetal Lung	lung
45	chr2:110325200-110330000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr2:110325200-110331000	Weak transcription	HSMM	muscle
47	chr2:110325200-110331000	Weak transcription	Osteobl	bone
48	chr2:110325200-110341000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:110325400-110330800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr2:110325400-110343800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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