Variant report

Variant	rs1787194
Chromosome Location	chr18:45386395-45386396
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10432199	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10502890	0.82[CEU][hapmap]
rs10853560	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11082638	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11082639	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11082641	0.83[CEU][hapmap]
rs11874858	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12457664	0.82[CEU][hapmap]
rs12458238	0.93[CEU][hapmap]
rs12604337	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12605333	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12956483	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12968107	0.96[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12968493	0.93[CEU][hapmap]
rs12969725	0.93[CEU][hapmap]
rs13381619	0.91[CHB][hapmap]
rs1539871	0.90[JPT][hapmap]
rs1539872	0.96[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1573362	0.80[CEU][hapmap]
rs1573363	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1613672	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1631576	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17741998	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1787176	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1787185	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1787186	0.96[CEU][hapmap]
rs1787193	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1787195	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1787196	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1787197	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1792653	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1792655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1792668	0.93[CEU][hapmap]
rs1792669	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1792670	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1792671	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1792672	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1792674	0.96[CEU][hapmap];0.80[EUR][1000 genomes]
rs1792675	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1792679	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1792680	0.80[EUR][1000 genomes]
rs1792681	0.92[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap]
rs1792682	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs1792683	0.92[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1792686	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs1792687	0.96[CEU][hapmap]
rs1792688	0.80[EUR][1000 genomes]
rs1981	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2000708	0.83[CEU][hapmap];0.82[CHB][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2000709	0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2012555	0.96[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2096932	0.93[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2096933	0.83[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28548478	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35710478	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3813068	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4939672	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4940102	0.93[CEU][hapmap]
rs4940109	0.85[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4940110	0.83[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4940120	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4940127	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61513611	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62086544	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6507790	0.89[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6507791	0.96[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap]
rs7228393	0.89[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7231538	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7232764	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7232893	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7233129	0.96[CEU][hapmap];0.82[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7236177	0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7237544	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7243502	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs729112	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs747952	0.96[CEU][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs747953	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs765213	0.88[CHB][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs8084915	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8095519	0.85[CEU][hapmap];0.87[CHB][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8097580	0.96[CEU][hapmap];0.92[CHB][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8097912	0.96[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8097925	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8099127	0.96[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8099681	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs948600	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs948601	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs948602	0.93[CEU][hapmap]
rs948603	0.96[CEU][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs948604	0.85[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9946556	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9950207	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9955626	0.96[CEU][hapmap];0.80[CHB][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9966637	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9966964	0.92[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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
17	nsv1059619	chr18:45384301-45401360	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv1066646	chr18:45384301-45406242	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv1057028	chr18:45384301-45410482	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1787194	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45345400-45400200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr18:45366200-45390000	Weak transcription	Colonic Mucosa	Colon
3	chr18:45366600-45408200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr18:45369800-45386400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr18:45372200-45396000	Weak transcription	NHLF	lung
6	chr18:45380600-45386800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr18:45381200-45386800	ZNF genes & repeats	Fetal Lung	lung
8	chr18:45381200-45387000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
9	chr18:45381600-45386600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
10	chr18:45381800-45386600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr18:45381800-45387800	ZNF genes & repeats	Dnd41	blood
12	chr18:45382200-45387000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr18:45382200-45420400	Weak transcription	Right Ventricle	heart
14	chr18:45382400-45386400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
15	chr18:45382400-45387600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr18:45382600-45389600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr18:45383000-45389600	Weak transcription	Fetal Heart	heart
18	chr18:45383000-45396600	Strong transcription	Hela-S3	cervix
19	chr18:45383400-45386400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr18:45383600-45386600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
21	chr18:45383600-45387000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
22	chr18:45383600-45392400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr18:45383800-45386400	ZNF genes & repeats	Primary B cells from cord blood	blood
24	chr18:45383800-45387400	ZNF genes & repeats	Primary T cells from cord blood	blood
25	chr18:45383800-45388400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr18:45383800-45388400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
27	chr18:45384000-45386600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
28	chr18:45384000-45386600	Strong transcription	Osteobl	bone
29	chr18:45384000-45386800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
30	chr18:45384000-45387000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr18:45384000-45387000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr18:45384000-45387000	ZNF genes & repeats	GM12878-XiMat	blood
33	chr18:45384000-45387400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
34	chr18:45384000-45388200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr18:45384200-45386400	Weak transcription	Esophagus	oesophagus
36	chr18:45384200-45386800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
37	chr18:45384200-45398800	Weak transcription	Pancreas	Pancrea
38	chr18:45384200-45421200	Weak transcription	Gastric	stomach
39	chr18:45384200-45423000	Weak transcription	Lung	lung
40	chr18:45384400-45386400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr18:45384400-45386400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr18:45384400-45386400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr18:45384400-45386400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr18:45384400-45386400	Weak transcription	Fetal Intestine Small	intestine
45	chr18:45384400-45386400	Strong transcription	Placenta	Placenta
46	chr18:45384400-45386400	Weak transcription	Fetal Stomach	stomach
47	chr18:45384400-45386400	Weak transcription	Ovary	ovary
48	chr18:45384400-45386400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr18:45384400-45386400	Weak transcription	Thymus	Thymus
50	chr18:45384400-45388000	Weak transcription	Skeletal Muscle Female	skeletal muscle

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