Variant report

Variant	rs948600
Chromosome Location	chr18:45429822-45429823
allele	C/T
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	chr18:45429095..45432024-chr18:45444733..45448383,3	MCF-7	breast:
4	chr18:45420997..45425237-chr18:45427977..45430649,5	K562	blood:

Variant related genes	Relation type
ENSG00000175387	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10432199	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10853560	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11082638	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11082639	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11874858	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12458238	0.81[EUR][1000 genomes]
rs12604337	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12605333	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12956483	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12968107	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12968493	0.81[EUR][1000 genomes]
rs13381619	0.87[ASN][1000 genomes]
rs1539872	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1573363	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1613672	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1631576	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17741998	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1787176	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1787193	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1787194	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1787195	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1787196	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1787197	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1787198	0.81[EUR][1000 genomes]
rs1792653	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1792655	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1792667	0.81[EUR][1000 genomes]
rs1792668	0.81[EUR][1000 genomes]
rs1792669	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1792670	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1792672	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1792675	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1792683	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1792687	0.80[EUR][1000 genomes]
rs2000708	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2000709	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2012555	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2096932	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2096933	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28548478	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35710478	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3813068	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4939672	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4940109	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4940110	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4940120	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4940127	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61513611	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62086544	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6507790	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7228393	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7231538	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7232764	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7232893	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7233129	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7236177	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7237544	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7243502	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs729112	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs747952	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs747953	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs765213	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8084915	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8095519	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8097580	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8097912	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8097925	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8099127	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8099681	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs948601	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs948603	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs948604	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9946556	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9950207	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9955626	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9966637	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9966964	0.91[AMR][1000 genomes];0.93[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
rs948600	SMAD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:87 , 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	chr18:45422200-45430600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr18:45423000-45430600	Weak transcription	NHLF	lung
12	chr18:45423000-45432800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr18:45423200-45430000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr18:45423200-45430600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr18:45423200-45430600	Weak transcription	Left Ventricle	heart
16	chr18:45423200-45430600	Weak transcription	Lung	lung
17	chr18:45423200-45430600	Weak transcription	Pancreas	Pancrea
18	chr18:45423200-45430600	Weak transcription	HSMM	muscle
19	chr18:45423200-45432800	Weak transcription	Duodenum Mucosa	Duodenum
20	chr18:45423200-45438200	Weak transcription	Gastric	stomach
21	chr18:45423200-45451400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr18:45424600-45431600	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr18:45424800-45431000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr18:45424800-45433000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr18:45425000-45430600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr18:45425400-45432600	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr18:45425600-45430000	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr18:45425800-45432800	Weak transcription	HMEC	breast
29	chr18:45426000-45433000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr18:45426200-45431000	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr18:45426200-45433000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr18:45426200-45438200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr18:45426400-45430600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr18:45426400-45430600	Weak transcription	Brain Hippocampus Middle	brain
35	chr18:45426400-45431600	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr18:45426400-45431600	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr18:45426400-45432800	Weak transcription	HepG2	liver
38	chr18:45426600-45433000	Weak transcription	NHEK	skin
39	chr18:45426800-45431200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
40	chr18:45427000-45431600	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr18:45427200-45430800	Weak transcription	Brain Anterior Caudate	brain
42	chr18:45427400-45430000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr18:45427600-45434200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr18:45428400-45433000	Weak transcription	Fetal Kidney	kidney
45	chr18:45428600-45430600	Weak transcription	Aorta	Aorta
46	chr18:45428600-45432600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr18:45428600-45432800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr18:45428600-45438000	Weak transcription	K562	blood
49	chr18:45429000-45430000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr18:45429000-45433800	ZNF genes & repeats	Primary B cells from peripheral blood	blood

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