Variant report

Variant	rs1749409
Chromosome Location	chr1:155870416-155870417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155861450..155863047-chr1:155868429..155870558,2	K562	blood:
2	chr1:155852352..155854119-chr1:155868160..155870548,2	K562	blood:
3	chr1:155863551..155866591-chr1:155868599..155871078,3	K562	blood:
4	chr1:155868953..155871356-chr1:155876102..155879060,2	MCF-7	breast:
5	chr1:155867375..155873348-chr1:155878269..155881617,9	K562	blood:

Variant related genes	Relation type
ENSG00000143622	Chromatin interaction
ENSG00000201614	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1010033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1018730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1055184	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10908485	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1094558	0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1094559	0.81[AFR][1000 genomes]
rs11264421	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12039053	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12129384	0.87[AFR][1000 genomes]
rs12138833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12747344	1.00[CEU][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs1544119	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap]
rs1749407	0.91[EUR][1000 genomes]
rs1749408	0.85[EUR][1000 genomes]
rs1765275	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1964951	0.94[EUR][1000 genomes]
rs2275071	0.90[ASN][1000 genomes]
rs2275079	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2275081	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2364402	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2364404	0.89[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28379575	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2886069	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34802187	0.97[EUR][1000 genomes]
rs35138477	0.84[EUR][1000 genomes]
rs35374730	0.97[EUR][1000 genomes]
rs35588936	0.89[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs35730001	0.94[EUR][1000 genomes]
rs3738587	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3768280	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4412586	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4661160	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4661162	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4661170	0.97[EUR][1000 genomes]
rs4661172	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.99[MKK][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs493446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506688	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs527113	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs536870	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572609	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs605025	1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6660802	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6667096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs708614	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628697	0.99[EUR][1000 genomes]
rs71628699	0.85[EUR][1000 genomes]
rs822502	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs822503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs822519	0.89[ASW][hapmap];1.00[CEU][hapmap]
rs822653	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1749409	MSTO1	cis	brain	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155844400-155874000	Weak transcription	Fetal Brain Male	brain
2	chr1:155850600-155873600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:155854400-155873600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:155862800-155873600	Weak transcription	Psoas Muscle	Psoas
5	chr1:155863400-155873600	Weak transcription	Stomach Mucosa	stomach
6	chr1:155863400-155880200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr1:155863800-155874000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:155865000-155875400	Strong transcription	Fetal Brain Female	brain
9	chr1:155865200-155871200	Strong transcription	HSMM	muscle
10	chr1:155865200-155878600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:155865200-155879200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:155865200-155879600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:155865400-155872000	Strong transcription	Muscle Satellite Cultured Cells	--
14	chr1:155865400-155873600	Strong transcription	Placenta	Placenta
15	chr1:155865600-155879200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:155865600-155879600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:155865800-155878400	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr1:155865800-155878800	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:155865800-155879200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:155865800-155879400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr1:155865800-155879800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:155865800-155880000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:155866000-155871800	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:155866000-155872000	Strong transcription	Osteobl	bone
25	chr1:155866000-155879000	Strong transcription	Liver	Liver
26	chr1:155866000-155879200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:155866000-155879200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:155866000-155879200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:155866000-155879600	Strong transcription	Primary B cells from peripheral blood	blood
30	chr1:155866000-155879600	Strong transcription	Duodenum Mucosa	Duodenum
31	chr1:155866000-155879600	Strong transcription	Fetal Intestine Large	intestine
32	chr1:155866000-155879800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr1:155866000-155879800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:155866000-155879800	Strong transcription	Fetal Thymus	thymus
35	chr1:155866200-155870600	Strong transcription	A549	lung
36	chr1:155866200-155871400	Strong transcription	NHLF	lung
37	chr1:155866200-155875400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:155866200-155879000	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr1:155866200-155879000	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr1:155866200-155879800	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:155866400-155870800	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr1:155866400-155871200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:155866400-155871800	Strong transcription	Primary B cells from cord blood	blood
44	chr1:155866400-155875400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr1:155866400-155877600	Strong transcription	Skeletal Muscle Male	skeletal muscle
46	chr1:155866400-155878000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr1:155866400-155879200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr1:155866400-155879600	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:155866400-155879800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr1:155866600-155872000	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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