Variant report

Variant	rs1792688
Chromosome Location	chr18:45368779-45368780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:45367366..45369056-chr18:45455430..45458300,2	MCF-7	breast:
2	chr18:45367507..45370509-chr18:45371769..45374946,4	K562	blood:
3	chr18:45368468..45370509-chr18:45372236..45375671,3	K562	blood:

Variant related genes	Relation type
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12454094	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12455876	0.81[EUR][1000 genomes]
rs12956483	0.84[EUR][1000 genomes]
rs1502606	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1613672	0.82[EUR][1000 genomes]
rs1623734	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1625400	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1627974	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1787176	0.81[EUR][1000 genomes]
rs1787180	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1787183	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1787185	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1787186	0.84[EUR][1000 genomes]
rs1787189	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1787190	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1787193	0.84[EUR][1000 genomes]
rs1787194	0.80[EUR][1000 genomes]
rs1792653	0.84[EUR][1000 genomes]
rs1792655	0.84[EUR][1000 genomes]
rs1792659	0.88[EUR][1000 genomes]
rs1792665	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1792671	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1792675	0.83[EUR][1000 genomes]
rs1792676	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1792677	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1792678	0.83[EUR][1000 genomes]
rs1792679	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1792680	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1792681	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792682	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792683	0.81[EUR][1000 genomes]
rs1792686	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1847173	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1981	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2047778	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2852972	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28548478	0.83[EUR][1000 genomes]
rs62086544	0.84[EUR][1000 genomes]
rs8099681	0.83[EUR][1000 genomes]
rs9946556	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057722	chr18:45343965-45401360	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv1058673	chr18:45360012-45404492	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv1059186	chr18:45360012-45407405	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1062894	chr18:45368587-45387738	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1066394	chr18:45368587-45394386	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv1060581	chr18:45368587-45397623	ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
7	nsv1057525	chr18:45368587-45407405	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1792688	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45340400-45369400	Weak transcription	Fetal Stomach	stomach
2	chr18:45342200-45384200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr18:45344000-45373000	Weak transcription	Pancreas	Pancrea
4	chr18:45345400-45400200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr18:45347600-45381800	Weak transcription	Right Ventricle	heart
6	chr18:45351000-45374600	Weak transcription	Brain Cingulate Gyrus	brain
7	chr18:45353000-45381200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr18:45354600-45381800	Weak transcription	Fetal Intestine Small	intestine
9	chr18:45354800-45370800	Weak transcription	Fetal Brain Male	brain
10	chr18:45355000-45368800	Weak transcription	Brain Germinal Matrix	brain
11	chr18:45355600-45375600	Strong transcription	Hela-S3	cervix
12	chr18:45355600-45375800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr18:45355600-45376200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr18:45356000-45378000	Weak transcription	Small Intestine	intestine
15	chr18:45356200-45377800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr18:45356200-45384000	Weak transcription	Spleen	Spleen
17	chr18:45356600-45376200	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr18:45357200-45370000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr18:45357200-45373200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr18:45358600-45376400	Strong transcription	Dnd41	blood
21	chr18:45358800-45382400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr18:45359000-45374400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr18:45359800-45370000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr18:45359800-45375600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr18:45359800-45375600	Strong transcription	Fetal Thymus	thymus
26	chr18:45360000-45373200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr18:45360000-45375400	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr18:45360000-45375600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr18:45361400-45375600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr18:45361400-45375600	Strong transcription	A549	lung
31	chr18:45361400-45376000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr18:45362400-45373000	Strong transcription	Placenta	Placenta
33	chr18:45362400-45375200	Strong transcription	Primary B cells from cord blood	blood
34	chr18:45362400-45375600	Strong transcription	Primary T helper cells PMA-I stimulated	--
35	chr18:45362600-45371800	Strong transcription	Liver	Liver
36	chr18:45362600-45372400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr18:45362600-45375600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr18:45363000-45370000	Strong transcription	Primary T cells from cord blood	blood
39	chr18:45363000-45375800	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr18:45363200-45371000	Weak transcription	HMEC	breast
41	chr18:45363400-45373600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr18:45363800-45369000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr18:45363800-45375600	Strong transcription	H1 Cell Line	embryonic stem cell
44	chr18:45363800-45375600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr18:45363800-45376400	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr18:45364000-45370000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr18:45364000-45372200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr18:45364000-45375400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr18:45364200-45369200	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr18:45364200-45370000	Strong transcription	Primary B cells from peripheral blood	blood

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