Variant report

Variant	rs1792686
Chromosome Location	chr18:45375785-45375786
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10502890	0.81[ASW][hapmap];0.81[CEU][hapmap];0.95[LWK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap]
rs10853560	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11082638	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs11082639	0.88[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs11082641	0.85[CEU][hapmap];0.95[YRI][hapmap]
rs12454094	0.88[EUR][1000 genomes]
rs12455876	0.85[EUR][1000 genomes]
rs12457664	0.81[ASW][hapmap];0.81[CEU][hapmap];0.95[LWK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap]
rs12458238	0.92[CEU][hapmap];0.95[YRI][hapmap]
rs12955534	0.82[EUR][1000 genomes]
rs12968107	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs12968493	0.92[CEU][hapmap];0.94[LWK][hapmap];0.91[TSI][hapmap];0.86[YRI][hapmap]
rs12969725	0.81[ASW][hapmap];0.92[CEU][hapmap];0.94[LWK][hapmap];0.89[TSI][hapmap];0.95[YRI][hapmap]
rs13381619	0.85[CHB][hapmap]
rs1502606	0.92[EUR][1000 genomes]
rs1539871	0.87[ASW][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap]
rs1539872	0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs1573362	0.81[CEU][hapmap];0.95[YRI][hapmap]
rs1573363	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs1613672	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1623734	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1625400	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1627974	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1631576	1.00[CEU][hapmap];0.92[GIH][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs17741998	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs1787176	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1787180	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1787183	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1787185	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1787186	0.87[ASW][hapmap];0.96[CEU][hapmap];0.92[LWK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1787189	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1787190	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1787193	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs1787194	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1787199	1.00[YRI][hapmap]
rs1792655	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1792658	0.89[LWK][hapmap];0.87[YRI][hapmap]
rs1792659	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1792663	0.82[EUR][1000 genomes]
rs1792664	0.82[EUR][1000 genomes]
rs1792665	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1792666	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs1792668	0.86[ASW][hapmap];0.92[CEU][hapmap];0.95[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs1792669	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs1792670	0.96[CEU][hapmap];0.82[CHB][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs1792671	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792674	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[LWK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap]
rs1792675	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1792676	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1792677	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1792678	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1792679	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792680	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792681	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792682	0.96[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1792683	0.92[CEU][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap]
rs1792684	0.87[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs1792687	0.87[ASW][hapmap];0.96[CEU][hapmap];0.92[LWK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap]
rs1792688	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1792689	0.95[YRI][hapmap]
rs1847173	0.92[EUR][1000 genomes]
rs1942158	0.95[YRI][hapmap]
rs1981	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2000708	0.85[CEU][hapmap]
rs2000709	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs2012555	0.94[ASW][hapmap];0.96[CEU][hapmap];0.88[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];0.87[YRI][hapmap]
rs2047778	0.86[EUR][1000 genomes]
rs2096932	0.82[JPT][hapmap]
rs2096933	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs2653659	0.84[EUR][1000 genomes]
rs2852972	0.92[EUR][1000 genomes]
rs3813068	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs4940102	0.92[CEU][hapmap]
rs4940109	0.85[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.82[TSI][hapmap]
rs4940110	0.85[CEU][hapmap];0.90[JPT][hapmap]
rs6507790	0.88[CEU][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.88[MEX][hapmap]
rs6507791	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs7228393	0.88[CEU][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs7231538	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs7233129	0.96[CEU][hapmap];0.82[JPT][hapmap];0.82[TSI][hapmap]
rs7236177	0.96[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap]
rs729112	0.96[CEU][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs747952	0.96[CEU][hapmap]
rs747953	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs765213	0.80[CEU][hapmap];0.81[CHB][hapmap]
rs8095519	0.85[CEU][hapmap];0.97[GIH][hapmap];0.89[MEX][hapmap]
rs8097580	0.95[CEU][hapmap]
rs8097912	0.96[CEU][hapmap];1.00[JPT][hapmap]
rs8099127	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs8671	0.88[AFR][1000 genomes]
rs948602	0.92[CEU][hapmap];0.95[YRI][hapmap]
rs948603	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs948604	0.85[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap]
rs9946556	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs9955626	0.96[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap]
rs9966964	0.92[CEU][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 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
8	nsv1064282	chr18:45369857-45404768	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
9	nsv1064797	chr18:45372027-45394386	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv1063859	chr18:45372027-45404492	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1062318	chr18:45374239-45394780	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv1055814	chr18:45374239-45395377	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv1057298	chr18:45374239-45404428	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1062731	chr18:45374239-45404768	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1058128	chr18:45374658-45394780	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv1065607	chr18:45374658-45404751	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1792686	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45342200-45384200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr18:45345400-45400200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr18:45347600-45381800	Weak transcription	Right Ventricle	heart
4	chr18:45353000-45381200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr18:45354600-45381800	Weak transcription	Fetal Intestine Small	intestine
6	chr18:45355600-45375800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr18:45355600-45376200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr18:45356000-45378000	Weak transcription	Small Intestine	intestine
9	chr18:45356200-45377800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:45356200-45384000	Weak transcription	Spleen	Spleen
11	chr18:45356600-45376200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr18:45358600-45376400	Strong transcription	Dnd41	blood
13	chr18:45358800-45382400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr18:45361400-45376000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr18:45363000-45375800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr18:45363800-45376400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr18:45364600-45376200	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr18:45365200-45375800	Strong transcription	Primary hematopoietic stem cells	blood
19	chr18:45365800-45381800	Weak transcription	Psoas Muscle	Psoas
20	chr18:45366000-45381800	Weak transcription	Aorta	Aorta
21	chr18:45366200-45390000	Weak transcription	Colonic Mucosa	Colon
22	chr18:45366400-45384000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr18:45366400-45384000	Weak transcription	Brain Angular Gyrus	brain
24	chr18:45366400-45384000	Weak transcription	Esophagus	oesophagus
25	chr18:45366600-45408200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr18:45368200-45375800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr18:45368200-45384000	Weak transcription	Stomach Mucosa	stomach
28	chr18:45368400-45377200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr18:45369000-45381800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr18:45369200-45381200	Weak transcription	Brain Germinal Matrix	brain
31	chr18:45369600-45380000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr18:45369600-45381800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr18:45369600-45382000	Weak transcription	Fetal Brain Female	brain
34	chr18:45369800-45383600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr18:45369800-45384000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr18:45369800-45384000	Weak transcription	Fetal Stomach	stomach
37	chr18:45369800-45386400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr18:45371600-45380400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr18:45371600-45381200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr18:45371800-45377000	Weak transcription	Brain Anterior Caudate	brain
41	chr18:45371800-45381200	Weak transcription	Brain Substantia Nigra	brain
42	chr18:45371800-45382000	Weak transcription	Fetal Heart	heart
43	chr18:45371800-45382200	Weak transcription	Fetal Brain Male	brain
44	chr18:45372000-45381400	Weak transcription	Brain Hippocampus Middle	brain
45	chr18:45372000-45381800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr18:45372000-45384000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr18:45372200-45381200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr18:45372200-45381800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr18:45372200-45381800	Weak transcription	Colon Smooth Muscle	Colon
50	chr18:45372200-45381800	Weak transcription	Lung	lung

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