Variant report

Variant	rs34557890
Chromosome Location	chr2:110316208-110316209
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:110315553..110317822-chr2:110320975..110322550,2	MCF-7	breast:
2	chr2:110310683..110312314-chr2:110314864..110316411,2	MCF-7	breast:
3	chr2:110315967..110317938-chr2:110370785..110372677,2	MCF-7	breast:
4	chr2:110314274..110316891-chr2:110317469..110319541,2	K562	blood:

Variant related genes	Relation type
ENSG00000186522	Chromatin interaction
ENSG00000198142	Chromatin interaction

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]
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]
rs56364682	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	0.87[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
rs34557890	SEPT10	cis	Muscle Skeletal	GTEx

Chromatin state (count:98 , 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	chr2:110299600-110318600	Weak transcription	Esophagus	oesophagus
6	chr2:110299600-110320200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr2:110299600-110324200	Weak transcription	Brain Angular Gyrus	brain
8	chr2:110301400-110325000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:110301600-110321000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:110302000-110333600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:110302200-110357600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:110302400-110343000	Weak transcription	Psoas Muscle	Psoas
13	chr2:110303000-110320400	Weak transcription	Brain Substantia Nigra	brain
14	chr2:110304200-110318800	Weak transcription	Colon Smooth Muscle	Colon
15	chr2:110304800-110320800	Weak transcription	Fetal Heart	heart
16	chr2:110307200-110322800	Weak transcription	Brain Anterior Caudate	brain
17	chr2:110308200-110317200	Weak transcription	Spleen	Spleen
18	chr2:110308400-110363400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:110308600-110358600	Weak transcription	Small Intestine	intestine
20	chr2:110309000-110347400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:110309800-110319800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:110309800-110323000	Weak transcription	Aorta	Aorta
23	chr2:110309800-110351600	Weak transcription	Pancreas	Pancrea
24	chr2:110310200-110318200	Weak transcription	NHLF	lung
25	chr2:110310200-110351600	Weak transcription	Fetal Brain Male	brain
26	chr2:110310400-110317000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr2:110310400-110317800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr2:110310400-110321000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr2:110310400-110323000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:110310400-110323000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:110310400-110337800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr2:110310400-110338400	Weak transcription	Lung	lung
33	chr2:110310400-110342000	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:110310400-110351600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:110310400-110351800	Weak transcription	Fetal Brain Female	brain
36	chr2:110310400-110353800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr2:110310400-110363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr2:110310600-110317000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr2:110310600-110341400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr2:110310800-110317000	Weak transcription	HSMMtube	muscle
41	chr2:110310800-110318200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr2:110310800-110320200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr2:110310800-110336800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr2:110312000-110317000	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr2:110312000-110317000	Weak transcription	HSMM	muscle
46	chr2:110312000-110318600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:110312000-110318600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:110312200-110321400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr2:110312200-110326000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr2:110312200-110328400	Weak transcription	Ovary	ovary

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