Variant report

Variant	rs35710478
Chromosome Location	chr18:45377882-45377883
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10432199	0.83[EUR][1000 genomes]
rs10853560	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11082638	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12956483	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12968107	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1539872	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1573363	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1613672	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1631576	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17741998	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1787176	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1787193	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1787194	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1787195	0.80[EUR][1000 genomes]
rs1787196	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1787197	0.88[EUR][1000 genomes]
rs1792653	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1792655	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1792669	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1792670	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1792672	0.85[EUR][1000 genomes]
rs1792675	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1792683	0.89[EUR][1000 genomes]
rs2012555	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2096932	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28548478	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3813068	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4940110	0.81[AMR][1000 genomes]
rs4940120	0.84[EUR][1000 genomes]
rs4940127	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62086544	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7231538	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7232764	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7232893	0.87[EUR][1000 genomes]
rs7233129	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7236177	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7237544	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs729112	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs747952	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs747953	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8084915	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8097580	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8097912	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8099127	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8099681	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs948600	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs948603	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9946556	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9950207	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9955626	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9966637	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9966964	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	esv3415287	chr18:45375954-45378452	Weak transcription Strong transcription ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs35710478	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 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	chr18:45356000-45378000	Weak transcription	Small Intestine	intestine
7	chr18:45356200-45384000	Weak transcription	Spleen	Spleen
8	chr18:45358800-45382400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr18:45365800-45381800	Weak transcription	Psoas Muscle	Psoas
10	chr18:45366000-45381800	Weak transcription	Aorta	Aorta
11	chr18:45366200-45390000	Weak transcription	Colonic Mucosa	Colon
12	chr18:45366400-45384000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr18:45366400-45384000	Weak transcription	Brain Angular Gyrus	brain
14	chr18:45366400-45384000	Weak transcription	Esophagus	oesophagus
15	chr18:45366600-45408200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr18:45368200-45384000	Weak transcription	Stomach Mucosa	stomach
17	chr18:45369000-45381800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr18:45369200-45381200	Weak transcription	Brain Germinal Matrix	brain
19	chr18:45369600-45380000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr18:45369600-45381800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr18:45369600-45382000	Weak transcription	Fetal Brain Female	brain
22	chr18:45369800-45383600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr18:45369800-45384000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr18:45369800-45384000	Weak transcription	Fetal Stomach	stomach
25	chr18:45369800-45386400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr18:45371600-45380400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr18:45371600-45381200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr18:45371800-45381200	Weak transcription	Brain Substantia Nigra	brain
29	chr18:45371800-45382000	Weak transcription	Fetal Heart	heart
30	chr18:45371800-45382200	Weak transcription	Fetal Brain Male	brain
31	chr18:45372000-45381400	Weak transcription	Brain Hippocampus Middle	brain
32	chr18:45372000-45381800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr18:45372000-45384000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr18:45372200-45381200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr18:45372200-45381800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr18:45372200-45381800	Weak transcription	Colon Smooth Muscle	Colon
37	chr18:45372200-45381800	Weak transcription	Lung	lung
38	chr18:45372200-45381800	Weak transcription	HSMMtube	muscle
39	chr18:45372200-45382400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr18:45372200-45386200	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr18:45372200-45396000	Weak transcription	NHLF	lung
42	chr18:45372400-45381400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr18:45373000-45381800	Weak transcription	Placenta	Placenta
44	chr18:45373200-45381800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr18:45373200-45381800	Weak transcription	Ovary	ovary
46	chr18:45373200-45381800	Weak transcription	Thymus	Thymus
47	chr18:45373200-45382000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr18:45373200-45382000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr18:45373200-45384000	Weak transcription	Gastric	stomach
50	chr18:45373200-45384000	Weak transcription	Pancreas	Pancrea

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