Variant report

Variant	rs4620750
Chromosome Location	chr18:45559960-45559961
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12605978	0.85[YRI][hapmap]
rs4359513	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4468699	0.88[EUR][1000 genomes]
rs4939701	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4940195	0.90[CHD][hapmap];0.82[ASN][1000 genomes]
rs4940197	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4940202	0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4940217	0.90[EUR][1000 genomes]
rs7226941	0.90[EUR][1000 genomes]
rs7243734	0.93[CHD][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs8093883	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8099419	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9945580	0.87[EUR][1000 genomes]
rs9951809	0.88[EUR][1000 genomes]
rs9958955	0.88[EUR][1000 genomes]
rs9960301	0.92[EUR][1000 genomes]
rs9960608	0.80[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	nsv909616	chr18:45467806-45844500	Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4620750	SMAD2	cis	parietal	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:45550400-45563400	Weak transcription	Stomach Mucosa	stomach
2	chr18:45550600-45564000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr18:45550800-45560200	Weak transcription	Gastric	stomach
4	chr18:45550800-45563000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr18:45551200-45561600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr18:45552600-45565200	Weak transcription	Colonic Mucosa	Colon
7	chr18:45554200-45563400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr18:45554200-45567800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr18:45554400-45560200	Weak transcription	Lung	lung
10	chr18:45554400-45562200	Weak transcription	Fetal Kidney	kidney
11	chr18:45554400-45563000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr18:45554400-45567600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr18:45554600-45560000	Weak transcription	Placenta	Placenta
14	chr18:45554600-45560800	Weak transcription	Brain Substantia Nigra	brain
15	chr18:45554800-45560200	Weak transcription	Fetal Stomach	stomach
16	chr18:45554800-45563400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr18:45555000-45563800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr18:45555000-45564000	Weak transcription	Adipose Nuclei	Adipose
19	chr18:45555400-45562200	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr18:45556200-45562600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr18:45557400-45570000	Weak transcription	Fetal Intestine Small	intestine
22	chr18:45557800-45560400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr18:45558200-45562800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr18:45558200-45563800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr18:45558400-45560200	Weak transcription	Esophagus	oesophagus
26	chr18:45558400-45560200	Weak transcription	Fetal Muscle Leg	muscle
27	chr18:45558400-45560200	Weak transcription	Spleen	Spleen
28	chr18:45558400-45578400	Weak transcription	Ovary	ovary
29	chr18:45559000-45565600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr18:45559200-45560800	Enhancers	HMEC	breast
31	chr18:45559200-45564400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr18:45559400-45560600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr18:45559400-45560600	Enhancers	HSMM	muscle
34	chr18:45559400-45560800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr18:45559400-45560800	Enhancers	NH-A	brain
36	chr18:45559600-45560400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr18:45559600-45560400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr18:45559600-45560400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr18:45559600-45560400	Enhancers	HSMMtube	muscle
40	chr18:45559600-45560400	Enhancers	NHEK	skin
41	chr18:45559600-45560400	Enhancers	Osteobl	bone
42	chr18:45559600-45560600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr18:45559600-45560800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr18:45559600-45560800	Enhancers	NHDF-Ad	bronchial
45	chr18:45559800-45560000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr18:45559800-45560600	Enhancers	Hela-S3	cervix
47	chr18:45559800-45565200	Enhancers	Breast Myoepithelial Primary Cells	Breast

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