Variant report

Variant	rs747952
Chromosome Location	chr18:45428977-45428978
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:45422820..45426374-chr18:45428189..45430649,3	K562	blood:
2	chr18:45428185..45429886-chr18:45431869..45434765,2	K562	blood:
3	chr18:45420997..45425237-chr18:45427977..45430649,5	K562	blood:

Variant related genes	Relation type
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10432199	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10502890	0.85[CEU][hapmap]
rs10853560	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11082638	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11082639	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11082641	0.86[CEU][hapmap]
rs11874858	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12457664	0.85[CEU][hapmap]
rs12458238	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs12604337	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12605333	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12956483	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12968107	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12968493	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs12969725	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs13381619	0.98[ASN][1000 genomes]
rs1539872	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1573362	0.83[CEU][hapmap]
rs1573363	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1613672	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1631576	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17741998	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1787176	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1787185	0.93[CEU][hapmap]
rs1787186	0.92[CEU][hapmap]
rs1787193	0.96[CEU][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1787194	0.96[CEU][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1787195	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1787196	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1787197	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1787198	0.83[EUR][1000 genomes]
rs1792653	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792655	0.96[CEU][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792667	0.83[EUR][1000 genomes]
rs1792668	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs1792669	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792670	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1792671	0.96[CEU][hapmap]
rs1792672	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1792674	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs1792675	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1792679	0.93[CEU][hapmap]
rs1792681	0.88[CEU][hapmap]
rs1792682	0.93[CEU][hapmap]
rs1792683	0.89[CEU][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1792686	0.96[CEU][hapmap]
rs1792687	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs1981	0.92[CEU][hapmap]
rs2000708	0.86[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2000709	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2012555	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2096932	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2096933	0.86[CEU][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28548478	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35710478	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3813068	0.96[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4939672	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4940102	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs4940109	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4940110	0.86[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4940120	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4940127	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61513611	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62086544	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6507790	0.93[CEU][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6507791	1.00[CEU][hapmap]
rs7228393	0.92[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7231538	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7232764	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7232893	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7233129	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7236177	1.00[CEU][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7237544	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7243502	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs729112	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs747953	1.00[CEU][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs765213	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8084915	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8095519	0.89[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8097580	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8097912	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8097925	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8099127	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8099681	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs948600	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs948601	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs948602	0.96[CEU][hapmap]
rs948603	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs948604	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9946556	0.96[CEU][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9947494	0.83[ASN][1000 genomes]
rs9950207	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9955626	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9966637	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9966964	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv909614	chr18:45419421-45478490	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs747952	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45397000-45430600	Weak transcription	Brain Angular Gyrus	brain
2	chr18:45400400-45432200	Weak transcription	Ovary	ovary
3	chr18:45420800-45433000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr18:45420800-45439600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr18:45421000-45430600	Weak transcription	Right Ventricle	heart
6	chr18:45421200-45436800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr18:45421800-45430400	Weak transcription	Esophagus	oesophagus
8	chr18:45421800-45430600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr18:45421800-45437800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr18:45422200-45429200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr18:45422200-45430600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr18:45423000-45430600	Weak transcription	NHLF	lung
13	chr18:45423000-45432800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr18:45423200-45429000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr18:45423200-45429200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr18:45423200-45429200	Weak transcription	Right Atrium	heart
17	chr18:45423200-45429200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr18:45423200-45430000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr18:45423200-45430600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr18:45423200-45430600	Weak transcription	Left Ventricle	heart
21	chr18:45423200-45430600	Weak transcription	Lung	lung
22	chr18:45423200-45430600	Weak transcription	Pancreas	Pancrea
23	chr18:45423200-45430600	Weak transcription	HSMM	muscle
24	chr18:45423200-45432800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr18:45423200-45438200	Weak transcription	Gastric	stomach
26	chr18:45423200-45451400	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr18:45424600-45431600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr18:45424800-45431000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr18:45424800-45433000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr18:45425000-45430600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr18:45425400-45432600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr18:45425600-45430000	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr18:45425800-45432800	Weak transcription	HMEC	breast
34	chr18:45426000-45433000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr18:45426200-45429200	Weak transcription	Brain Substantia Nigra	brain
36	chr18:45426200-45429200	Weak transcription	Fetal Lung	lung
37	chr18:45426200-45429800	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr18:45426200-45431000	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr18:45426200-45433000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr18:45426200-45438200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr18:45426400-45429000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr18:45426400-45429200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr18:45426400-45429800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr18:45426400-45430600	Weak transcription	Brain Cingulate Gyrus	brain
45	chr18:45426400-45430600	Weak transcription	Brain Hippocampus Middle	brain
46	chr18:45426400-45431600	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr18:45426400-45431600	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr18:45426400-45432800	Weak transcription	HepG2	liver
49	chr18:45426600-45433000	Weak transcription	NHEK	skin
50	chr18:45426800-45431200	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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